Starting phenix.real_space_refine on Tue Jun 25 05:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/06_2024/8s32_19687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/06_2024/8s32_19687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/06_2024/8s32_19687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/06_2024/8s32_19687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/06_2024/8s32_19687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/06_2024/8s32_19687.pdb" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 294 5.16 5 C 34636 2.51 5 N 9562 2.21 5 O 11060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 354": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 354": "OE1" <-> "OE2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 354": "OE1" <-> "OE2" Residue "G GLU 396": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 354": "OE1" <-> "OE2" Residue "H GLU 396": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I GLU 354": "OE1" <-> "OE2" Residue "I GLU 396": "OE1" <-> "OE2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J GLU 354": "OE1" <-> "OE2" Residue "J GLU 396": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 354": "OE1" <-> "OE2" Residue "K GLU 396": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L GLU 396": "OE1" <-> "OE2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M GLU 354": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "N GLU 60": "OE1" <-> "OE2" Residue "N GLU 354": "OE1" <-> "OE2" Residue "N GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 55552 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "B" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "C" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "D" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "E" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "F" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "G" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "H" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "I" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "J" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "K" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "L" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "M" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "N" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "O" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "P" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "Q" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "R" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "S" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "T" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "U" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "V" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "W" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "X" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "Y" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "Z" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "1" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Chain: "2" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Time building chain proxies: 24.72, per 1000 atoms: 0.44 Number of scatterers: 55552 At special positions: 0 Unit cell: (155.767, 155.767, 159.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 294 16.00 O 11060 8.00 N 9562 7.00 C 34636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.94 Conformation dependent library (CDL) restraints added in 7.6 seconds 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13608 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 98 sheets defined 58.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 109 Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 337 through 354 Processing helix chain 'A' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 496 through 515 Processing helix chain 'B' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.699A pdb=" N MET B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.621A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 337 through 354 Processing helix chain 'B' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 496 through 515 Processing helix chain 'C' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 109 Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.699A pdb=" N MET C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Proline residue: C 234 - end of helix Processing helix chain 'C' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 460 through 471 Processing helix chain 'C' and resid 496 through 515 Processing helix chain 'D' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.621A pdb=" N GLU D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 109 Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Proline residue: D 234 - end of helix Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'D' and resid 337 through 354 Processing helix chain 'D' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 409 Processing helix chain 'D' and resid 415 through 425 Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'D' and resid 496 through 515 Processing helix chain 'E' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 85 removed outlier: 3.594A pdb=" N VAL E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 109 Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'E' and resid 337 through 354 Processing helix chain 'E' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 Processing helix chain 'E' and resid 415 through 425 Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'E' and resid 496 through 515 Processing helix chain 'F' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 109 Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY F 158 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.826A pdb=" N PHE F 203 " --> pdb=" O SER F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) Proline residue: F 234 - end of helix Processing helix chain 'F' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 311 Processing helix chain 'F' and resid 337 through 354 Processing helix chain 'F' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY F 374 " --> pdb=" O LYS F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 Processing helix chain 'F' and resid 415 through 425 Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 460 through 471 Processing helix chain 'F' and resid 496 through 515 Processing helix chain 'G' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL G 76 " --> pdb=" O MET G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 109 Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE G 203 " --> pdb=" O SER G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) Proline residue: G 234 - end of helix Processing helix chain 'G' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS G 285 " --> pdb=" O GLY G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 311 Processing helix chain 'G' and resid 337 through 354 Processing helix chain 'G' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY G 374 " --> pdb=" O LYS G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 409 Processing helix chain 'G' and resid 415 through 425 Processing helix chain 'G' and resid 432 through 446 Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 460 through 471 Processing helix chain 'G' and resid 496 through 515 Processing helix chain 'H' and resid 8 through 28 removed outlier: 4.224A pdb=" N VAL H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 85 removed outlier: 3.596A pdb=" N VAL H 76 " --> pdb=" O MET H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 109 Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 139 through 151 Processing helix chain 'H' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY H 158 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE H 203 " --> pdb=" O SER H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Proline residue: H 234 - end of helix Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU H 261 " --> pdb=" O ALA H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS H 285 " --> pdb=" O GLY H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 311 Processing helix chain 'H' and resid 337 through 354 Processing helix chain 'H' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY H 374 " --> pdb=" O LYS H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 409 Processing helix chain 'H' and resid 415 through 425 Processing helix chain 'H' and resid 432 through 446 Processing helix chain 'H' and resid 447 through 458 Processing helix chain 'H' and resid 460 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'I' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL I 28 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU I 58 " --> pdb=" O SER I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 109 Processing helix chain 'I' and resid 111 through 134 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE I 203 " --> pdb=" O SER I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET I 232 " --> pdb=" O ASN I 228 " (cutoff:3.500A) Proline residue: I 234 - end of helix Processing helix chain 'I' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS I 285 " --> pdb=" O GLY I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 311 Processing helix chain 'I' and resid 337 through 354 Processing helix chain 'I' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY I 374 " --> pdb=" O LYS I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 409 Processing helix chain 'I' and resid 415 through 425 Processing helix chain 'I' and resid 432 through 446 Processing helix chain 'I' and resid 447 through 458 Processing helix chain 'I' and resid 460 through 471 Processing helix chain 'I' and resid 496 through 515 Processing helix chain 'J' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 59 removed outlier: 3.621A pdb=" N GLU J 58 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL J 76 " --> pdb=" O MET J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 111 through 134 Processing helix chain 'J' and resid 139 through 151 Processing helix chain 'J' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE J 203 " --> pdb=" O SER J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET J 232 " --> pdb=" O ASN J 228 " (cutoff:3.500A) Proline residue: J 234 - end of helix Processing helix chain 'J' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU J 261 " --> pdb=" O ALA J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 311 Processing helix chain 'J' and resid 337 through 354 Processing helix chain 'J' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 409 Processing helix chain 'J' and resid 415 through 425 Processing helix chain 'J' and resid 432 through 446 Processing helix chain 'J' and resid 447 through 458 Processing helix chain 'J' and resid 460 through 471 Processing helix chain 'J' and resid 496 through 515 Processing helix chain 'K' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL K 76 " --> pdb=" O MET K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 109 Processing helix chain 'K' and resid 111 through 134 Processing helix chain 'K' and resid 139 through 151 Processing helix chain 'K' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE K 203 " --> pdb=" O SER K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 242 removed outlier: 3.699A pdb=" N MET K 232 " --> pdb=" O ASN K 228 " (cutoff:3.500A) Proline residue: K 234 - end of helix Processing helix chain 'K' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU K 261 " --> pdb=" O ALA K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS K 285 " --> pdb=" O GLY K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 311 Processing helix chain 'K' and resid 337 through 354 Processing helix chain 'K' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY K 374 " --> pdb=" O LYS K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 409 Processing helix chain 'K' and resid 415 through 425 Processing helix chain 'K' and resid 432 through 446 Processing helix chain 'K' and resid 447 through 458 Processing helix chain 'K' and resid 460 through 471 Processing helix chain 'K' and resid 496 through 515 Processing helix chain 'L' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL L 76 " --> pdb=" O MET L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 109 Processing helix chain 'L' and resid 111 through 134 Processing helix chain 'L' and resid 139 through 151 Processing helix chain 'L' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY L 158 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE L 203 " --> pdb=" O SER L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET L 232 " --> pdb=" O ASN L 228 " (cutoff:3.500A) Proline residue: L 234 - end of helix Processing helix chain 'L' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU L 261 " --> pdb=" O ALA L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 311 Processing helix chain 'L' and resid 337 through 354 Processing helix chain 'L' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY L 374 " --> pdb=" O LYS L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 409 Processing helix chain 'L' and resid 415 through 425 Processing helix chain 'L' and resid 432 through 446 Processing helix chain 'L' and resid 447 through 458 Processing helix chain 'L' and resid 460 through 471 Processing helix chain 'L' and resid 496 through 515 Processing helix chain 'M' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL M 28 " --> pdb=" O ASP M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU M 58 " --> pdb=" O SER M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL M 76 " --> pdb=" O MET M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 109 Processing helix chain 'M' and resid 111 through 134 Processing helix chain 'M' and resid 139 through 151 Processing helix chain 'M' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 204 removed outlier: 3.826A pdb=" N PHE M 203 " --> pdb=" O SER M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET M 232 " --> pdb=" O ASN M 228 " (cutoff:3.500A) Proline residue: M 234 - end of helix Processing helix chain 'M' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU M 261 " --> pdb=" O ALA M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS M 285 " --> pdb=" O GLY M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 311 Processing helix chain 'M' and resid 337 through 354 Processing helix chain 'M' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY M 374 " --> pdb=" O LYS M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 384 through 409 Processing helix chain 'M' and resid 415 through 425 Processing helix chain 'M' and resid 432 through 446 Processing helix chain 'M' and resid 447 through 458 Processing helix chain 'M' and resid 460 through 471 Processing helix chain 'M' and resid 496 through 515 Processing helix chain 'N' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 59 removed outlier: 3.621A pdb=" N GLU N 58 " --> pdb=" O SER N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL N 76 " --> pdb=" O MET N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 109 Processing helix chain 'N' and resid 111 through 134 Processing helix chain 'N' and resid 139 through 151 Processing helix chain 'N' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY N 158 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE N 203 " --> pdb=" O SER N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) Proline residue: N 234 - end of helix Processing helix chain 'N' and resid 257 through 268 removed outlier: 3.621A pdb=" N LEU N 261 " --> pdb=" O ALA N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS N 285 " --> pdb=" O GLY N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'N' and resid 337 through 354 Processing helix chain 'N' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY N 374 " --> pdb=" O LYS N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 384 through 409 Processing helix chain 'N' and resid 415 through 425 Processing helix chain 'N' and resid 432 through 446 Processing helix chain 'N' and resid 447 through 458 Processing helix chain 'N' and resid 460 through 471 Processing helix chain 'N' and resid 496 through 515 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 7.549A pdb=" N VAL G 38 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET A 519 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 7.552A pdb=" N ASN A 36 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET B 519 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 38 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 521 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY A 334 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY A 334 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 218 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 249 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 220 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 246 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 275 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE A 248 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 49 removed outlier: 7.550A pdb=" N ASN B 36 " --> pdb=" O GLU C 517 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N MET C 519 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 38 " --> pdb=" O MET C 519 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR C 521 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY B 334 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY B 334 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 218 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 249 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 220 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 246 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 275 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE B 248 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 removed outlier: 7.548A pdb=" N ASN C 36 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET D 519 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 38 " --> pdb=" O MET D 519 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR D 521 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 178 Processing sheet with id=AB7, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY C 334 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY C 334 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE C 218 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 249 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 220 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 246 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL C 275 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 248 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AC2, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.549A pdb=" N ASN D 36 " --> pdb=" O GLU E 517 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET E 519 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL D 38 " --> pdb=" O MET E 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR E 521 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 173 through 178 Processing sheet with id=AC4, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY D 334 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY D 334 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE D 218 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 249 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU D 220 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU D 246 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 275 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE D 248 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 49 removed outlier: 7.535A pdb=" N ASN E 36 " --> pdb=" O GLU F 517 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET F 519 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 38 " --> pdb=" O MET F 519 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR F 521 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 173 through 178 Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY E 334 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY E 334 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE E 218 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE E 249 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU E 220 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU E 246 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL E 275 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE E 248 " --> pdb=" O VAL E 275 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AD4, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AD5, first strand: chain 'F' and resid 47 through 49 removed outlier: 7.548A pdb=" N ASN F 36 " --> pdb=" O GLU G 517 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET G 519 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL F 38 " --> pdb=" O MET G 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR G 521 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 173 through 178 Processing sheet with id=AD7, first strand: chain 'F' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY F 334 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY F 334 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE F 218 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 249 " --> pdb=" O PHE F 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 220 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU F 246 " --> pdb=" O ALA F 273 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL F 275 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE F 248 " --> pdb=" O VAL F 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AE1, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AE2, first strand: chain 'G' and resid 173 through 178 Processing sheet with id=AE3, first strand: chain 'G' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY G 334 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY G 334 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE G 218 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE G 249 " --> pdb=" O PHE G 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU G 220 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 246 " --> pdb=" O ALA G 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL G 275 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE G 248 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AE6, first strand: chain 'G' and resid 475 through 478 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 removed outlier: 7.554A pdb=" N VAL N 38 " --> pdb=" O GLU H 517 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET H 519 " --> pdb=" O VAL N 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 47 through 49 removed outlier: 7.549A pdb=" N ASN H 36 " --> pdb=" O GLU I 517 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N MET I 519 " --> pdb=" O ASN H 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL H 38 " --> pdb=" O MET I 519 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR I 521 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 173 through 178 Processing sheet with id=AF1, first strand: chain 'H' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY H 334 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA H 319 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY H 334 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA H 319 " --> pdb=" O GLY H 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE H 218 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE H 249 " --> pdb=" O PHE H 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU H 220 " --> pdb=" O ILE H 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU H 246 " --> pdb=" O ALA H 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL H 275 " --> pdb=" O LEU H 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE H 248 " --> pdb=" O VAL H 275 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 410 through 412 Processing sheet with id=AF4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AF5, first strand: chain 'I' and resid 47 through 49 removed outlier: 7.546A pdb=" N ASN I 36 " --> pdb=" O GLU J 517 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET J 519 " --> pdb=" O ASN I 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 38 " --> pdb=" O MET J 519 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N THR J 521 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 173 through 178 Processing sheet with id=AF7, first strand: chain 'I' and resid 192 through 194 removed outlier: 6.146A pdb=" N GLY I 334 " --> pdb=" O ALA I 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA I 319 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 192 through 194 removed outlier: 6.146A pdb=" N GLY I 334 " --> pdb=" O ALA I 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA I 319 " --> pdb=" O GLY I 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE I 218 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE I 249 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU I 220 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU I 246 " --> pdb=" O ALA I 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL I 275 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE I 248 " --> pdb=" O VAL I 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 410 through 412 Processing sheet with id=AG1, first strand: chain 'I' and resid 475 through 478 Processing sheet with id=AG2, first strand: chain 'J' and resid 47 through 49 removed outlier: 7.539A pdb=" N ASN J 36 " --> pdb=" O GLU K 517 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET K 519 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL J 38 " --> pdb=" O MET K 519 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR K 521 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 173 through 178 Processing sheet with id=AG4, first strand: chain 'J' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY J 334 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA J 319 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY J 334 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA J 319 " --> pdb=" O GLY J 334 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE J 218 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE J 249 " --> pdb=" O PHE J 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU J 220 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU J 246 " --> pdb=" O ALA J 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL J 275 " --> pdb=" O LEU J 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE J 248 " --> pdb=" O VAL J 275 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 410 through 412 Processing sheet with id=AG7, first strand: chain 'J' and resid 475 through 478 Processing sheet with id=AG8, first strand: chain 'K' and resid 47 through 49 removed outlier: 7.548A pdb=" N ASN K 36 " --> pdb=" O GLU L 517 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N MET L 519 " --> pdb=" O ASN K 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL K 38 " --> pdb=" O MET L 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR L 521 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 173 through 178 Processing sheet with id=AH1, first strand: chain 'K' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY K 334 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA K 319 " --> pdb=" O GLY K 334 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY K 334 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA K 319 " --> pdb=" O GLY K 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE K 218 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE K 249 " --> pdb=" O PHE K 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU K 220 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU K 246 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL K 275 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE K 248 " --> pdb=" O VAL K 275 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 410 through 412 Processing sheet with id=AH4, first strand: chain 'K' and resid 475 through 478 Processing sheet with id=AH5, first strand: chain 'L' and resid 47 through 49 removed outlier: 7.550A pdb=" N ASN L 36 " --> pdb=" O GLU M 517 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N MET M 519 " --> pdb=" O ASN L 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL L 38 " --> pdb=" O MET M 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR M 521 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 173 through 178 Processing sheet with id=AH7, first strand: chain 'L' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY L 334 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA L 319 " --> pdb=" O GLY L 334 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY L 334 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA L 319 " --> pdb=" O GLY L 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE L 218 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE L 249 " --> pdb=" O PHE L 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU L 220 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU L 246 " --> pdb=" O ALA L 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL L 275 " --> pdb=" O LEU L 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE L 248 " --> pdb=" O VAL L 275 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 410 through 412 Processing sheet with id=AI1, first strand: chain 'L' and resid 475 through 478 Processing sheet with id=AI2, first strand: chain 'M' and resid 47 through 49 removed outlier: 7.551A pdb=" N ASN M 36 " --> pdb=" O GLU N 517 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET N 519 " --> pdb=" O ASN M 36 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL M 38 " --> pdb=" O MET N 519 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR N 521 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 173 through 178 Processing sheet with id=AI4, first strand: chain 'M' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY M 334 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA M 319 " --> pdb=" O GLY M 334 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY M 334 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA M 319 " --> pdb=" O GLY M 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE M 218 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE M 249 " --> pdb=" O PHE M 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU M 220 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU M 246 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL M 275 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE M 248 " --> pdb=" O VAL M 275 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 410 through 412 Processing sheet with id=AI7, first strand: chain 'M' and resid 475 through 478 Processing sheet with id=AI8, first strand: chain 'N' and resid 173 through 178 Processing sheet with id=AI9, first strand: chain 'N' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY N 334 " --> pdb=" O ALA N 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA N 319 " --> pdb=" O GLY N 334 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY N 334 " --> pdb=" O ALA N 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA N 319 " --> pdb=" O GLY N 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE N 218 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE N 249 " --> pdb=" O PHE N 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU N 220 " --> pdb=" O ILE N 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU N 246 " --> pdb=" O ALA N 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL N 275 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE N 248 " --> pdb=" O VAL N 275 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 410 through 412 Processing sheet with id=AJ3, first strand: chain 'N' and resid 475 through 478 Processing sheet with id=AJ4, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AJ5, first strand: chain 'P' and resid 19 through 20 Processing sheet with id=AJ6, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AJ7, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ8, first strand: chain 'S' and resid 19 through 20 Processing sheet with id=AJ9, first strand: chain 'T' and resid 19 through 20 Processing sheet with id=AK1, first strand: chain 'U' and resid 19 through 20 Processing sheet with id=AK2, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AK3, first strand: chain 'W' and resid 19 through 20 Processing sheet with id=AK4, first strand: chain 'X' and resid 19 through 20 Processing sheet with id=AK5, first strand: chain 'Y' and resid 19 through 20 Processing sheet with id=AK6, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AK7, first strand: chain '1' and resid 19 through 20 Processing sheet with id=AK8, first strand: chain '2' and resid 19 through 20 3824 hydrogen bonds defined for protein. 10884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.55 Time building geometry restraints manager: 19.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 19166 1.34 - 1.46: 9944 1.46 - 1.58: 26386 1.58 - 1.70: 0 1.70 - 1.82: 546 Bond restraints: 56042 Sorted by residual: bond pdb=" N MET L 388 " pdb=" CA MET L 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.67e+00 bond pdb=" N MET F 388 " pdb=" CA MET F 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.67e+00 bond pdb=" N MET D 388 " pdb=" CA MET D 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.65e+00 bond pdb=" N MET B 388 " pdb=" CA MET B 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.63e+00 bond pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.58e+00 ... (remaining 56037 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.13: 1101 106.13 - 113.09: 32045 113.09 - 120.05: 18660 120.05 - 127.00: 23612 127.00 - 133.96: 294 Bond angle restraints: 75712 Sorted by residual: angle pdb=" CA GLU M 396 " pdb=" CB GLU M 396 " pdb=" CG GLU M 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU F 396 " pdb=" CB GLU F 396 " pdb=" CG GLU F 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU G 396 " pdb=" CB GLU G 396 " pdb=" CG GLU G 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU B 396 " pdb=" CB GLU B 396 " pdb=" CG GLU B 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU H 396 " pdb=" CB GLU H 396 " pdb=" CG GLU H 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 75707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 29957 16.80 - 33.60: 3149 33.60 - 50.39: 1096 50.39 - 67.19: 322 67.19 - 83.99: 126 Dihedral angle restraints: 34650 sinusoidal: 13454 harmonic: 21196 Sorted by residual: dihedral pdb=" CA ILE J 59 " pdb=" C ILE J 59 " pdb=" N GLU J 60 " pdb=" CA GLU J 60 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ILE C 59 " pdb=" C ILE C 59 " pdb=" N GLU C 60 " pdb=" CA GLU C 60 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ILE G 59 " pdb=" C ILE G 59 " pdb=" N GLU G 60 " pdb=" CA GLU G 60 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 34647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5760 0.031 - 0.062: 2191 0.062 - 0.093: 773 0.093 - 0.125: 388 0.125 - 0.156: 30 Chirality restraints: 9142 Sorted by residual: chirality pdb=" CA MET B 388 " pdb=" N MET B 388 " pdb=" C MET B 388 " pdb=" CB MET B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA MET F 388 " pdb=" N MET F 388 " pdb=" C MET F 388 " pdb=" CB MET F 388 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA MET C 388 " pdb=" N MET C 388 " pdb=" C MET C 388 " pdb=" CB MET C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 9139 not shown) Planarity restraints: 9884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU J 256 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C GLU J 256 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU J 256 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA J 257 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 256 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C GLU I 256 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU I 256 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA I 257 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 256 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C GLU M 256 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU M 256 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA M 257 " 0.009 2.00e-02 2.50e+03 ... (remaining 9881 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9261 2.76 - 3.30: 57192 3.30 - 3.83: 97412 3.83 - 4.37: 105873 4.37 - 4.90: 186704 Nonbonded interactions: 456442 Sorted by model distance: nonbonded pdb=" OD2 ASP C 154 " pdb=" OG1 THR C 156 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP K 154 " pdb=" OG1 THR K 156 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP B 154 " pdb=" OG1 THR B 156 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP E 154 " pdb=" OG1 THR E 156 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP D 154 " pdb=" OG1 THR D 156 " model vdw 2.225 2.440 ... (remaining 456437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 30.160 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 118.660 Find NCS groups from input model: 3.650 Set up NCS constraints: 0.780 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 56042 Z= 0.248 Angle : 0.596 7.068 75712 Z= 0.315 Chirality : 0.041 0.156 9142 Planarity : 0.003 0.023 9884 Dihedral : 16.855 83.990 21042 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.19 % Rotamer: Outliers : 1.61 % Allowed : 23.87 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.10), residues: 7462 helix: 2.50 (0.08), residues: 4144 sheet: 0.14 (0.18), residues: 896 loop : -0.49 (0.11), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 23 HIS 0.001 0.000 HIS 2 26 PHE 0.007 0.001 PHE B 194 TYR 0.005 0.001 TYR J 505 ARG 0.003 0.000 ARG J 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1394 time to evaluate : 4.453 Fit side-chains REVERT: A 17 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6293 (tmt-80) REVERT: A 75 GLU cc_start: 0.7396 (tp30) cc_final: 0.6923 (tp30) REVERT: A 163 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7336 (mt-10) REVERT: A 165 MET cc_start: 0.7647 (mtm) cc_final: 0.7248 (mtt) REVERT: A 177 GLU cc_start: 0.6423 (tp30) cc_final: 0.5992 (tt0) REVERT: A 192 MET cc_start: 0.7097 (ppp) cc_final: 0.6869 (ppp) REVERT: A 224 LYS cc_start: 0.6163 (ttpp) cc_final: 0.5845 (pttp) REVERT: A 380 VAL cc_start: 0.7831 (m) cc_final: 0.7526 (m) REVERT: A 400 HIS cc_start: 0.7221 (m-70) cc_final: 0.6967 (t-90) REVERT: A 403 ARG cc_start: 0.7067 (ttm-80) cc_final: 0.6821 (ttp-170) REVERT: A 444 ARG cc_start: 0.7825 (ttp80) cc_final: 0.6812 (tpt90) REVERT: A 483 GLU cc_start: 0.7286 (pt0) cc_final: 0.7008 (mt-10) REVERT: B 17 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6302 (tmt-80) REVERT: B 75 GLU cc_start: 0.7377 (tp30) cc_final: 0.6914 (tp30) REVERT: B 163 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7410 (mt-10) REVERT: B 165 MET cc_start: 0.7655 (mtm) cc_final: 0.7216 (mtt) REVERT: B 177 GLU cc_start: 0.6447 (tp30) cc_final: 0.5948 (tt0) REVERT: B 192 MET cc_start: 0.7048 (ppp) cc_final: 0.6769 (ppp) REVERT: B 224 LYS cc_start: 0.6192 (ttpp) cc_final: 0.5876 (pttp) REVERT: B 380 VAL cc_start: 0.7796 (m) cc_final: 0.7521 (m) REVERT: B 400 HIS cc_start: 0.7253 (m-70) cc_final: 0.6997 (t-90) REVERT: B 403 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: B 444 ARG cc_start: 0.7856 (ttp80) cc_final: 0.6800 (tpt90) REVERT: C 17 ARG cc_start: 0.7144 (ttp-110) cc_final: 0.6351 (tmt-80) REVERT: C 75 GLU cc_start: 0.7413 (tp30) cc_final: 0.7093 (tp30) REVERT: C 163 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7407 (mt-10) REVERT: C 165 MET cc_start: 0.7669 (mtm) cc_final: 0.7163 (mtt) REVERT: C 177 GLU cc_start: 0.6477 (tp30) cc_final: 0.6060 (tt0) REVERT: C 192 MET cc_start: 0.7067 (ppp) cc_final: 0.6783 (ppp) REVERT: C 193 GLN cc_start: 0.7409 (pt0) cc_final: 0.7179 (pt0) REVERT: C 224 LYS cc_start: 0.6176 (ttpp) cc_final: 0.5916 (pttp) REVERT: C 380 VAL cc_start: 0.7861 (m) cc_final: 0.7516 (m) REVERT: C 400 HIS cc_start: 0.7214 (m-70) cc_final: 0.6964 (t-90) REVERT: C 444 ARG cc_start: 0.7828 (ttp80) cc_final: 0.6824 (tpt90) REVERT: C 494 ASP cc_start: 0.7932 (m-30) cc_final: 0.7703 (m-30) REVERT: D 17 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6279 (tmt-80) REVERT: D 75 GLU cc_start: 0.7403 (tp30) cc_final: 0.6968 (tp30) REVERT: D 163 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7401 (mt-10) REVERT: D 165 MET cc_start: 0.7643 (mtm) cc_final: 0.7257 (mtt) REVERT: D 177 GLU cc_start: 0.6432 (tp30) cc_final: 0.5999 (tt0) REVERT: D 192 MET cc_start: 0.7088 (ppp) cc_final: 0.6887 (ppp) REVERT: D 224 LYS cc_start: 0.6164 (ttpp) cc_final: 0.5809 (pttp) REVERT: D 380 VAL cc_start: 0.7847 (m) cc_final: 0.7555 (m) REVERT: D 400 HIS cc_start: 0.7308 (m-70) cc_final: 0.7024 (t-90) REVERT: D 403 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6864 (ttp-170) REVERT: D 444 ARG cc_start: 0.7819 (ttp80) cc_final: 0.6800 (tpt90) REVERT: E 17 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6356 (tmt-80) REVERT: E 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.7014 (tp30) REVERT: E 165 MET cc_start: 0.7665 (mtm) cc_final: 0.7285 (mtt) REVERT: E 177 GLU cc_start: 0.6391 (tp30) cc_final: 0.5949 (tt0) REVERT: E 192 MET cc_start: 0.7044 (ppp) cc_final: 0.6819 (ppp) REVERT: E 193 GLN cc_start: 0.7349 (pt0) cc_final: 0.7143 (pt0) REVERT: E 224 LYS cc_start: 0.6099 (ttpp) cc_final: 0.5755 (pttp) REVERT: E 380 VAL cc_start: 0.7809 (m) cc_final: 0.7479 (m) REVERT: E 400 HIS cc_start: 0.7216 (m-70) cc_final: 0.6939 (t-90) REVERT: E 403 ARG cc_start: 0.7048 (ttm-80) cc_final: 0.6824 (ttp-170) REVERT: E 444 ARG cc_start: 0.7838 (ttp80) cc_final: 0.6797 (tpt90) REVERT: F 17 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6318 (tmt-80) REVERT: F 72 MET cc_start: 0.8350 (mtp) cc_final: 0.7895 (mtm) REVERT: F 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.6962 (tp30) REVERT: F 163 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7431 (mt-10) REVERT: F 165 MET cc_start: 0.7760 (mtm) cc_final: 0.7211 (mtt) REVERT: F 177 GLU cc_start: 0.6436 (tp30) cc_final: 0.5896 (tt0) REVERT: F 192 MET cc_start: 0.7059 (ppp) cc_final: 0.6802 (ppp) REVERT: F 193 GLN cc_start: 0.7396 (pt0) cc_final: 0.7169 (pt0) REVERT: F 224 LYS cc_start: 0.6246 (ttpp) cc_final: 0.5973 (pttp) REVERT: F 380 VAL cc_start: 0.7841 (m) cc_final: 0.7533 (m) REVERT: F 400 HIS cc_start: 0.7274 (m-70) cc_final: 0.7051 (t-90) REVERT: F 403 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6783 (ttp-170) REVERT: F 444 ARG cc_start: 0.7789 (ttp80) cc_final: 0.6734 (tpt90) REVERT: G 17 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6274 (tmt-80) REVERT: G 75 GLU cc_start: 0.7378 (tp30) cc_final: 0.6872 (tp30) REVERT: G 163 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7335 (mt-10) REVERT: G 165 MET cc_start: 0.7685 (mtm) cc_final: 0.7161 (mtt) REVERT: G 177 GLU cc_start: 0.6490 (tp30) cc_final: 0.6004 (tt0) REVERT: G 192 MET cc_start: 0.7063 (ppp) cc_final: 0.6857 (ppp) REVERT: G 193 GLN cc_start: 0.7406 (pt0) cc_final: 0.7141 (pt0) REVERT: G 224 LYS cc_start: 0.6105 (ttpp) cc_final: 0.5795 (pttp) REVERT: G 380 VAL cc_start: 0.7893 (m) cc_final: 0.7623 (m) REVERT: G 400 HIS cc_start: 0.7276 (m-70) cc_final: 0.7027 (t-90) REVERT: G 403 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6754 (ttp-170) REVERT: G 444 ARG cc_start: 0.7843 (ttp80) cc_final: 0.6882 (tpt170) REVERT: H 17 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6311 (tmt-80) REVERT: H 75 GLU cc_start: 0.7396 (tp30) cc_final: 0.6923 (tp30) REVERT: H 163 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7336 (mt-10) REVERT: H 165 MET cc_start: 0.7649 (mtm) cc_final: 0.7248 (mtt) REVERT: H 177 GLU cc_start: 0.6420 (tp30) cc_final: 0.5986 (tt0) REVERT: H 192 MET cc_start: 0.7096 (ppp) cc_final: 0.6869 (ppp) REVERT: H 224 LYS cc_start: 0.6163 (ttpp) cc_final: 0.5846 (pttp) REVERT: H 380 VAL cc_start: 0.7840 (m) cc_final: 0.7538 (m) REVERT: H 400 HIS cc_start: 0.7227 (m-70) cc_final: 0.6971 (t-90) REVERT: H 403 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6823 (ttp-170) REVERT: H 444 ARG cc_start: 0.7824 (ttp80) cc_final: 0.6813 (tpt90) REVERT: H 483 GLU cc_start: 0.7287 (pt0) cc_final: 0.7009 (mt-10) REVERT: I 17 ARG cc_start: 0.7119 (ttp-110) cc_final: 0.6326 (tmt-80) REVERT: I 75 GLU cc_start: 0.7389 (tp30) cc_final: 0.6912 (tp30) REVERT: I 163 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7370 (mt-10) REVERT: I 165 MET cc_start: 0.7648 (mtm) cc_final: 0.7206 (mtt) REVERT: I 177 GLU cc_start: 0.6452 (tp30) cc_final: 0.5950 (tt0) REVERT: I 192 MET cc_start: 0.7049 (ppp) cc_final: 0.6768 (ppp) REVERT: I 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5909 (pttp) REVERT: I 380 VAL cc_start: 0.7814 (m) cc_final: 0.7546 (m) REVERT: I 400 HIS cc_start: 0.7285 (m-70) cc_final: 0.6983 (t-90) REVERT: I 403 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6797 (ttp-170) REVERT: I 444 ARG cc_start: 0.7851 (ttp80) cc_final: 0.6798 (tpt90) REVERT: J 17 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6356 (tmt-80) REVERT: J 75 GLU cc_start: 0.7414 (tp30) cc_final: 0.7095 (tp30) REVERT: J 163 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7408 (mt-10) REVERT: J 165 MET cc_start: 0.7653 (mtm) cc_final: 0.7154 (mtt) REVERT: J 177 GLU cc_start: 0.6487 (tp30) cc_final: 0.6055 (tt0) REVERT: J 192 MET cc_start: 0.7083 (ppp) cc_final: 0.6801 (ppp) REVERT: J 193 GLN cc_start: 0.7385 (pt0) cc_final: 0.7157 (pt0) REVERT: J 224 LYS cc_start: 0.6196 (ttpp) cc_final: 0.5951 (pttp) REVERT: J 380 VAL cc_start: 0.7871 (m) cc_final: 0.7527 (m) REVERT: J 400 HIS cc_start: 0.7203 (m-70) cc_final: 0.6955 (t-90) REVERT: J 444 ARG cc_start: 0.7824 (ttp80) cc_final: 0.6815 (tpt90) REVERT: J 494 ASP cc_start: 0.7954 (m-30) cc_final: 0.7748 (m-30) REVERT: K 17 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6269 (tmt-80) REVERT: K 75 GLU cc_start: 0.7390 (tp30) cc_final: 0.6961 (tp30) REVERT: K 163 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7391 (mt-10) REVERT: K 165 MET cc_start: 0.7643 (mtm) cc_final: 0.7267 (mtt) REVERT: K 177 GLU cc_start: 0.6441 (tp30) cc_final: 0.5989 (tt0) REVERT: K 192 MET cc_start: 0.7090 (ppp) cc_final: 0.6884 (ppp) REVERT: K 224 LYS cc_start: 0.6150 (ttpp) cc_final: 0.5783 (pttp) REVERT: K 380 VAL cc_start: 0.7834 (m) cc_final: 0.7540 (m) REVERT: K 400 HIS cc_start: 0.7274 (m-70) cc_final: 0.7013 (t-90) REVERT: K 403 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6866 (ttp-170) REVERT: K 444 ARG cc_start: 0.7812 (ttp80) cc_final: 0.6771 (tpt90) REVERT: L 17 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6346 (tmt-80) REVERT: L 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.6982 (tp30) REVERT: L 165 MET cc_start: 0.7712 (mtm) cc_final: 0.7308 (mtt) REVERT: L 177 GLU cc_start: 0.6376 (tp30) cc_final: 0.5928 (tt0) REVERT: L 192 MET cc_start: 0.7030 (ppp) cc_final: 0.6813 (ppp) REVERT: L 224 LYS cc_start: 0.6106 (ttpp) cc_final: 0.5760 (pttp) REVERT: L 380 VAL cc_start: 0.7835 (m) cc_final: 0.7509 (m) REVERT: L 400 HIS cc_start: 0.7213 (m-70) cc_final: 0.6936 (t-90) REVERT: L 403 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6817 (ttp-170) REVERT: L 444 ARG cc_start: 0.7826 (ttp80) cc_final: 0.6783 (tpt90) REVERT: M 17 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6321 (tmt-80) REVERT: M 72 MET cc_start: 0.8348 (mtp) cc_final: 0.7904 (mtm) REVERT: M 75 GLU cc_start: 0.7408 (tp30) cc_final: 0.6948 (tp30) REVERT: M 163 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7407 (mt-10) REVERT: M 165 MET cc_start: 0.7742 (mtm) cc_final: 0.7198 (mtt) REVERT: M 177 GLU cc_start: 0.6416 (tp30) cc_final: 0.5880 (tt0) REVERT: M 192 MET cc_start: 0.7069 (ppp) cc_final: 0.6807 (ppp) REVERT: M 193 GLN cc_start: 0.7385 (pt0) cc_final: 0.7145 (pt0) REVERT: M 224 LYS cc_start: 0.6248 (ttpp) cc_final: 0.5973 (pttp) REVERT: M 380 VAL cc_start: 0.7823 (m) cc_final: 0.7516 (m) REVERT: M 400 HIS cc_start: 0.7288 (m-70) cc_final: 0.7058 (t-90) REVERT: M 403 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.6793 (ttp-170) REVERT: M 444 ARG cc_start: 0.7803 (ttp80) cc_final: 0.6742 (tpt90) REVERT: M 483 GLU cc_start: 0.7211 (pt0) cc_final: 0.6994 (mt-10) REVERT: N 17 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6297 (tmt-80) REVERT: N 75 GLU cc_start: 0.7392 (tp30) cc_final: 0.6883 (tp30) REVERT: N 163 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7342 (mt-10) REVERT: N 165 MET cc_start: 0.7674 (mtm) cc_final: 0.7216 (mtt) REVERT: N 177 GLU cc_start: 0.6491 (tp30) cc_final: 0.6016 (tt0) REVERT: N 192 MET cc_start: 0.7058 (ppp) cc_final: 0.6805 (ppp) REVERT: N 193 GLN cc_start: 0.7418 (pt0) cc_final: 0.7133 (pt0) REVERT: N 224 LYS cc_start: 0.6108 (ttpp) cc_final: 0.5846 (pttp) REVERT: N 320 LYS cc_start: 0.6838 (tptt) cc_final: 0.6630 (tppt) REVERT: N 380 VAL cc_start: 0.7865 (m) cc_final: 0.7592 (m) REVERT: N 400 HIS cc_start: 0.7267 (m-70) cc_final: 0.7033 (t-90) REVERT: N 403 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6750 (ttp-170) REVERT: N 444 ARG cc_start: 0.7858 (ttp80) cc_final: 0.6883 (tpt170) REVERT: T 19 MET cc_start: 0.2668 (tpt) cc_final: 0.2439 (mmt) REVERT: Z 19 MET cc_start: 0.2738 (tpt) cc_final: 0.2526 (mmt) REVERT: 1 19 MET cc_start: 0.2680 (tpt) cc_final: 0.2437 (mmt) outliers start: 94 outliers final: 31 residues processed: 1450 average time/residue: 1.5012 time to fit residues: 2682.2898 Evaluate side-chains 948 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 917 time to evaluate : 5.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 232 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 329 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 626 optimal weight: 2.9990 chunk 562 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 300 optimal weight: 3.9990 chunk 581 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 353 optimal weight: 0.2980 chunk 432 optimal weight: 4.9990 chunk 673 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 365 GLN B 36 ASN C 36 ASN C 365 GLN D 36 ASN D 365 GLN E 36 ASN F 36 ASN F 365 GLN G 36 ASN G 365 GLN H 36 ASN H 365 GLN I 36 ASN J 36 ASN J 365 GLN K 36 ASN K 365 GLN L 36 ASN M 36 ASN M 365 GLN N 36 ASN N 365 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56042 Z= 0.232 Angle : 0.590 8.074 75712 Z= 0.304 Chirality : 0.043 0.162 9142 Planarity : 0.004 0.040 9884 Dihedral : 4.573 46.155 7959 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.12 % Favored : 97.69 % Rotamer: Outliers : 5.63 % Allowed : 25.17 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 7462 helix: 2.23 (0.08), residues: 4228 sheet: -0.16 (0.16), residues: 952 loop : -0.49 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 23 HIS 0.003 0.001 HIS P 26 PHE 0.006 0.001 PHE M 194 TYR 0.010 0.001 TYR J 505 ARG 0.003 0.000 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 986 time to evaluate : 4.565 Fit side-chains REVERT: A 17 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6433 (tmt-80) REVERT: A 75 GLU cc_start: 0.7395 (tp30) cc_final: 0.6946 (tp30) REVERT: A 184 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: A 192 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7062 (ppp) REVERT: A 213 GLU cc_start: 0.7008 (mp0) cc_final: 0.6729 (mp0) REVERT: A 224 LYS cc_start: 0.6275 (ttpp) cc_final: 0.5950 (pttp) REVERT: A 380 VAL cc_start: 0.7886 (m) cc_final: 0.7643 (m) REVERT: A 397 ASP cc_start: 0.6820 (m-30) cc_final: 0.6561 (t0) REVERT: A 400 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6947 (t-90) REVERT: A 403 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6775 (ttp-170) REVERT: A 444 ARG cc_start: 0.7909 (ttp80) cc_final: 0.6823 (tpt90) REVERT: A 483 GLU cc_start: 0.7270 (pt0) cc_final: 0.7020 (mt-10) REVERT: B 17 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6424 (tmt-80) REVERT: B 75 GLU cc_start: 0.7373 (tp30) cc_final: 0.6931 (tp30) REVERT: B 110 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.6743 (mtm) REVERT: B 143 ILE cc_start: 0.7618 (mm) cc_final: 0.7409 (mm) REVERT: B 184 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6346 (m-30) REVERT: B 192 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6977 (ppp) REVERT: B 213 GLU cc_start: 0.6985 (mp0) cc_final: 0.6557 (mp0) REVERT: B 224 LYS cc_start: 0.6288 (ttpp) cc_final: 0.5878 (pttp) REVERT: B 380 VAL cc_start: 0.7867 (m) cc_final: 0.7625 (m) REVERT: B 397 ASP cc_start: 0.6764 (m-30) cc_final: 0.6458 (t0) REVERT: B 400 HIS cc_start: 0.7354 (m-70) cc_final: 0.6991 (t-90) REVERT: B 403 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6780 (ttp-170) REVERT: C 17 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6453 (tmt-80) REVERT: C 75 GLU cc_start: 0.7431 (tp30) cc_final: 0.7084 (tp30) REVERT: C 79 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7796 (ttpt) REVERT: C 165 MET cc_start: 0.7417 (mtm) cc_final: 0.7117 (mtt) REVERT: C 184 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.6367 (m-30) REVERT: C 192 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6974 (ppp) REVERT: C 193 GLN cc_start: 0.7590 (pt0) cc_final: 0.7336 (pt0) REVERT: C 213 GLU cc_start: 0.6958 (mp0) cc_final: 0.6512 (mp0) REVERT: C 224 LYS cc_start: 0.6248 (ttpp) cc_final: 0.5797 (pttp) REVERT: C 327 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5387 (t70) REVERT: C 380 VAL cc_start: 0.7886 (m) cc_final: 0.7674 (m) REVERT: C 397 ASP cc_start: 0.6903 (m-30) cc_final: 0.6595 (t0) REVERT: C 400 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: D 12 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6389 (mtp180) REVERT: D 17 ARG cc_start: 0.7185 (ttp-110) cc_final: 0.6387 (tmt-80) REVERT: D 75 GLU cc_start: 0.7398 (tp30) cc_final: 0.6925 (tp30) REVERT: D 165 MET cc_start: 0.7420 (mtm) cc_final: 0.7212 (mtt) REVERT: D 184 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6374 (m-30) REVERT: D 213 GLU cc_start: 0.7073 (mp0) cc_final: 0.6752 (mp0) REVERT: D 224 LYS cc_start: 0.6300 (ttpp) cc_final: 0.5819 (pttp) REVERT: D 380 VAL cc_start: 0.7921 (m) cc_final: 0.7686 (m) REVERT: D 397 ASP cc_start: 0.6829 (m-30) cc_final: 0.6561 (t0) REVERT: D 403 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6788 (ttp-170) REVERT: E 12 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6416 (mtp180) REVERT: E 17 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.6462 (tmt-80) REVERT: E 75 GLU cc_start: 0.7441 (tp30) cc_final: 0.6911 (tp30) REVERT: E 79 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7786 (ttpt) REVERT: E 184 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6381 (m-30) REVERT: E 190 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7231 (mm-30) REVERT: E 192 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6939 (ppp) REVERT: E 193 GLN cc_start: 0.7513 (pt0) cc_final: 0.7266 (pt0) REVERT: E 213 GLU cc_start: 0.7033 (mp0) cc_final: 0.6765 (mp0) REVERT: E 224 LYS cc_start: 0.6206 (ttpp) cc_final: 0.5865 (pttp) REVERT: E 225 LYS cc_start: 0.7252 (mtmm) cc_final: 0.6647 (mtpp) REVERT: E 380 VAL cc_start: 0.7914 (m) cc_final: 0.7672 (m) REVERT: E 397 ASP cc_start: 0.6844 (m-30) cc_final: 0.6546 (t0) REVERT: E 400 HIS cc_start: 0.7311 (m-70) cc_final: 0.6968 (t-90) REVERT: F 12 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6319 (mtp180) REVERT: F 17 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6394 (tmt-80) REVERT: F 75 GLU cc_start: 0.7426 (tp30) cc_final: 0.6926 (tp30) REVERT: F 79 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7796 (ttpt) REVERT: F 184 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: F 193 GLN cc_start: 0.7536 (pt0) cc_final: 0.7283 (pt0) REVERT: F 213 GLU cc_start: 0.7070 (mp0) cc_final: 0.6685 (mp0) REVERT: F 224 LYS cc_start: 0.6321 (ttpp) cc_final: 0.5967 (pttp) REVERT: F 225 LYS cc_start: 0.7202 (mtmm) cc_final: 0.6582 (mtpp) REVERT: F 380 VAL cc_start: 0.7894 (m) cc_final: 0.7665 (m) REVERT: F 397 ASP cc_start: 0.6867 (m-30) cc_final: 0.6595 (t0) REVERT: F 400 HIS cc_start: 0.7310 (m-70) cc_final: 0.7013 (t-90) REVERT: F 403 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6788 (ttp-170) REVERT: F 444 ARG cc_start: 0.7908 (ttp80) cc_final: 0.6801 (tpt90) REVERT: G 12 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6615 (mtp180) REVERT: G 17 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6462 (tmt-80) REVERT: G 75 GLU cc_start: 0.7391 (tp30) cc_final: 0.6859 (tp30) REVERT: G 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7788 (ttpt) REVERT: G 165 MET cc_start: 0.7451 (mtm) cc_final: 0.7121 (mtt) REVERT: G 184 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6361 (m-30) REVERT: G 193 GLN cc_start: 0.7560 (pt0) cc_final: 0.7303 (pt0) REVERT: G 213 GLU cc_start: 0.7103 (mp0) cc_final: 0.6740 (mp0) REVERT: G 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5770 (pttp) REVERT: G 380 VAL cc_start: 0.7918 (m) cc_final: 0.7650 (m) REVERT: G 397 ASP cc_start: 0.6819 (m-30) cc_final: 0.6512 (t0) REVERT: G 400 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.7021 (t-90) REVERT: G 403 ARG cc_start: 0.7004 (ttm-80) cc_final: 0.6717 (ttp-170) REVERT: H 17 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: H 75 GLU cc_start: 0.7393 (tp30) cc_final: 0.6943 (tp30) REVERT: H 184 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6379 (m-30) REVERT: H 192 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7058 (ppp) REVERT: H 213 GLU cc_start: 0.7009 (mp0) cc_final: 0.6732 (mp0) REVERT: H 224 LYS cc_start: 0.6274 (ttpp) cc_final: 0.5951 (pttp) REVERT: H 380 VAL cc_start: 0.7890 (m) cc_final: 0.7654 (m) REVERT: H 397 ASP cc_start: 0.6818 (m-30) cc_final: 0.6558 (t0) REVERT: H 400 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6947 (t-90) REVERT: H 403 ARG cc_start: 0.7066 (ttm-80) cc_final: 0.6775 (ttp-170) REVERT: H 444 ARG cc_start: 0.7908 (ttp80) cc_final: 0.6824 (tpt90) REVERT: H 483 GLU cc_start: 0.7271 (pt0) cc_final: 0.7022 (mt-10) REVERT: I 12 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6429 (mtp180) REVERT: I 17 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: I 75 GLU cc_start: 0.7376 (tp30) cc_final: 0.6929 (tp30) REVERT: I 110 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.6756 (mtm) REVERT: I 143 ILE cc_start: 0.7652 (mm) cc_final: 0.7446 (mm) REVERT: I 184 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: I 192 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7006 (ppp) REVERT: I 213 GLU cc_start: 0.6965 (mp0) cc_final: 0.6536 (mp0) REVERT: I 224 LYS cc_start: 0.6292 (ttpp) cc_final: 0.5880 (pttp) REVERT: I 380 VAL cc_start: 0.7896 (m) cc_final: 0.7652 (m) REVERT: I 397 ASP cc_start: 0.6790 (m-30) cc_final: 0.6482 (t0) REVERT: I 400 HIS cc_start: 0.7342 (m-70) cc_final: 0.6969 (t-90) REVERT: I 403 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6783 (ttp-170) REVERT: J 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6447 (tmt-80) REVERT: J 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.7073 (tp30) REVERT: J 79 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7801 (ttpt) REVERT: J 165 MET cc_start: 0.7386 (mtm) cc_final: 0.7045 (mtt) REVERT: J 184 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: J 192 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6972 (ppp) REVERT: J 193 GLN cc_start: 0.7576 (pt0) cc_final: 0.7323 (pt0) REVERT: J 213 GLU cc_start: 0.6964 (mp0) cc_final: 0.6536 (mp0) REVERT: J 224 LYS cc_start: 0.6247 (ttpp) cc_final: 0.5816 (pttp) REVERT: J 380 VAL cc_start: 0.7895 (m) cc_final: 0.7694 (m) REVERT: J 397 ASP cc_start: 0.6895 (m-30) cc_final: 0.6586 (t0) REVERT: J 400 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: K 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6392 (mtp180) REVERT: K 17 ARG cc_start: 0.7183 (ttp-110) cc_final: 0.6382 (tmt-80) REVERT: K 75 GLU cc_start: 0.7393 (tp30) cc_final: 0.6923 (tp30) REVERT: K 165 MET cc_start: 0.7423 (mtm) cc_final: 0.7209 (mtt) REVERT: K 184 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6381 (m-30) REVERT: K 213 GLU cc_start: 0.7078 (mp0) cc_final: 0.6752 (mp0) REVERT: K 224 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5812 (pttp) REVERT: K 380 VAL cc_start: 0.7900 (m) cc_final: 0.7663 (m) REVERT: K 397 ASP cc_start: 0.6820 (m-30) cc_final: 0.6551 (t0) REVERT: K 400 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.7019 (t-90) REVERT: K 403 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6788 (ttp-170) REVERT: L 12 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6419 (mtp180) REVERT: L 17 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: L 75 GLU cc_start: 0.7441 (tp30) cc_final: 0.6907 (tp30) REVERT: L 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (ttpt) REVERT: L 184 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6400 (m-30) REVERT: L 190 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7244 (mm-30) REVERT: L 192 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6934 (ppp) REVERT: L 213 GLU cc_start: 0.7106 (mp0) cc_final: 0.6797 (mp0) REVERT: L 224 LYS cc_start: 0.6228 (ttpp) cc_final: 0.5882 (pttp) REVERT: L 225 LYS cc_start: 0.7267 (mtmm) cc_final: 0.6662 (mtpp) REVERT: L 226 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6403 (tp) REVERT: L 380 VAL cc_start: 0.7903 (m) cc_final: 0.7664 (m) REVERT: L 397 ASP cc_start: 0.6850 (m-30) cc_final: 0.6549 (t0) REVERT: L 400 HIS cc_start: 0.7303 (m-70) cc_final: 0.6961 (t-90) REVERT: M 12 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6307 (mtp180) REVERT: M 17 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6416 (tmt-80) REVERT: M 75 GLU cc_start: 0.7432 (tp30) cc_final: 0.6922 (tp30) REVERT: M 79 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7789 (ttpt) REVERT: M 184 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6357 (m-30) REVERT: M 193 GLN cc_start: 0.7509 (pt0) cc_final: 0.7250 (pt0) REVERT: M 213 GLU cc_start: 0.7082 (mp0) cc_final: 0.6689 (mp0) REVERT: M 224 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5919 (pttp) REVERT: M 225 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6574 (mtpp) REVERT: M 327 ASP cc_start: 0.5550 (OUTLIER) cc_final: 0.5304 (t70) REVERT: M 380 VAL cc_start: 0.7878 (m) cc_final: 0.7648 (m) REVERT: M 397 ASP cc_start: 0.6879 (m-30) cc_final: 0.6605 (t0) REVERT: M 400 HIS cc_start: 0.7314 (m-70) cc_final: 0.7020 (t-90) REVERT: M 403 ARG cc_start: 0.7065 (ttm-80) cc_final: 0.6785 (ttp-170) REVERT: M 444 ARG cc_start: 0.7897 (ttp80) cc_final: 0.6781 (tpt90) REVERT: M 483 GLU cc_start: 0.7203 (pt0) cc_final: 0.6970 (mt-10) REVERT: N 12 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6590 (mtp180) REVERT: N 17 ARG cc_start: 0.7203 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: N 75 GLU cc_start: 0.7400 (tp30) cc_final: 0.6856 (tp30) REVERT: N 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: N 165 MET cc_start: 0.7376 (mtm) cc_final: 0.6934 (mtt) REVERT: N 184 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6350 (m-30) REVERT: N 193 GLN cc_start: 0.7565 (pt0) cc_final: 0.7307 (pt0) REVERT: N 213 GLU cc_start: 0.7123 (mp0) cc_final: 0.6727 (mp0) REVERT: N 224 LYS cc_start: 0.6188 (ttpp) cc_final: 0.5772 (pttp) REVERT: N 380 VAL cc_start: 0.7918 (m) cc_final: 0.7652 (m) REVERT: N 397 ASP cc_start: 0.6818 (m-30) cc_final: 0.6515 (t0) REVERT: N 400 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: N 403 ARG cc_start: 0.7008 (ttm-80) cc_final: 0.6719 (ttp-170) outliers start: 328 outliers final: 121 residues processed: 1188 average time/residue: 1.3774 time to fit residues: 2054.3449 Evaluate side-chains 1062 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 890 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 318 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 232 MET Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 232 MET Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 184 ASP Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 308 LEU Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 232 MET Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 232 MET Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 374 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 560 optimal weight: 5.9990 chunk 458 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 675 optimal weight: 4.9990 chunk 729 optimal weight: 10.0000 chunk 601 optimal weight: 7.9990 chunk 669 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 541 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN D 365 GLN F 365 GLN G 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 56042 Z= 0.217 Angle : 0.540 7.493 75712 Z= 0.283 Chirality : 0.042 0.153 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.505 42.488 7948 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 5.70 % Allowed : 24.85 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.10), residues: 7462 helix: 2.26 (0.08), residues: 4228 sheet: -0.09 (0.15), residues: 1106 loop : -0.40 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 23 HIS 0.002 0.001 HIS E 400 PHE 0.009 0.001 PHE 2 25 TYR 0.011 0.001 TYR C 505 ARG 0.004 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 904 time to evaluate : 4.597 Fit side-chains REVERT: A 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6412 (tmt-80) REVERT: A 75 GLU cc_start: 0.7443 (tp30) cc_final: 0.6946 (tp30) REVERT: A 79 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (ttpt) REVERT: A 184 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: A 192 MET cc_start: 0.7358 (ppp) cc_final: 0.6999 (ppp) REVERT: A 213 GLU cc_start: 0.7020 (mp0) cc_final: 0.6621 (mp0) REVERT: A 224 LYS cc_start: 0.6338 (ttpp) cc_final: 0.5948 (pttp) REVERT: A 266 MET cc_start: 0.6764 (mmm) cc_final: 0.6555 (mtm) REVERT: A 327 ASP cc_start: 0.5597 (OUTLIER) cc_final: 0.5370 (t70) REVERT: A 397 ASP cc_start: 0.6840 (m-30) cc_final: 0.6582 (t0) REVERT: A 400 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6909 (t-90) REVERT: A 403 ARG cc_start: 0.7037 (ttm-80) cc_final: 0.6718 (ttp-170) REVERT: A 444 ARG cc_start: 0.7932 (ttp80) cc_final: 0.6835 (tpt90) REVERT: A 483 GLU cc_start: 0.7225 (pt0) cc_final: 0.6964 (mt-10) REVERT: B 17 ARG cc_start: 0.7240 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: B 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.6941 (tp30) REVERT: B 79 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7642 (mtmm) REVERT: B 184 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: B 213 GLU cc_start: 0.6983 (mp0) cc_final: 0.6555 (mp0) REVERT: B 224 LYS cc_start: 0.6283 (ttpp) cc_final: 0.5782 (pttp) REVERT: B 397 ASP cc_start: 0.6764 (m-30) cc_final: 0.6475 (t0) REVERT: B 400 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6981 (t-90) REVERT: B 403 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6737 (ttp-170) REVERT: C 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: C 75 GLU cc_start: 0.7418 (tp30) cc_final: 0.6975 (tp30) REVERT: C 79 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: C 165 MET cc_start: 0.7281 (mtp) cc_final: 0.6987 (mtt) REVERT: C 184 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6462 (m-30) REVERT: C 213 GLU cc_start: 0.6983 (mp0) cc_final: 0.6545 (mp0) REVERT: C 224 LYS cc_start: 0.6300 (ttpp) cc_final: 0.5891 (pttp) REVERT: C 327 ASP cc_start: 0.5543 (OUTLIER) cc_final: 0.5320 (t70) REVERT: C 397 ASP cc_start: 0.6877 (m-30) cc_final: 0.6575 (t0) REVERT: C 400 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: D 12 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6331 (mtp180) REVERT: D 17 ARG cc_start: 0.7204 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: D 75 GLU cc_start: 0.7417 (tp30) cc_final: 0.6946 (tp30) REVERT: D 165 MET cc_start: 0.7376 (mtp) cc_final: 0.7152 (mtt) REVERT: D 184 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: D 213 GLU cc_start: 0.7064 (mp0) cc_final: 0.6653 (mp0) REVERT: D 224 LYS cc_start: 0.6316 (ttpp) cc_final: 0.5824 (pttp) REVERT: D 327 ASP cc_start: 0.5581 (OUTLIER) cc_final: 0.5313 (t70) REVERT: D 397 ASP cc_start: 0.6860 (m-30) cc_final: 0.6546 (t0) REVERT: D 400 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: D 403 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6779 (ttp-170) REVERT: E 12 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6358 (mtp180) REVERT: E 17 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6473 (tmt-80) REVERT: E 75 GLU cc_start: 0.7496 (tp30) cc_final: 0.6994 (tp30) REVERT: E 79 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: E 184 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6454 (m-30) REVERT: E 190 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7282 (mm-30) REVERT: E 193 GLN cc_start: 0.7514 (pt0) cc_final: 0.7304 (pt0) REVERT: E 213 GLU cc_start: 0.7020 (mp0) cc_final: 0.6594 (mp0) REVERT: E 224 LYS cc_start: 0.6160 (ttpp) cc_final: 0.5716 (pttp) REVERT: E 327 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.5361 (t70) REVERT: E 397 ASP cc_start: 0.6797 (m-30) cc_final: 0.6514 (t0) REVERT: E 400 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6978 (t-90) REVERT: F 12 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.6306 (mtp180) REVERT: F 17 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: F 75 GLU cc_start: 0.7475 (tp30) cc_final: 0.6964 (tp30) REVERT: F 79 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7781 (ttpt) REVERT: F 184 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6439 (m-30) REVERT: F 213 GLU cc_start: 0.7025 (mp0) cc_final: 0.6558 (mp0) REVERT: F 224 LYS cc_start: 0.6235 (ttpp) cc_final: 0.5943 (pttp) REVERT: F 266 MET cc_start: 0.6663 (mmm) cc_final: 0.6386 (mmm) REVERT: F 327 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5382 (t70) REVERT: F 397 ASP cc_start: 0.6804 (m-30) cc_final: 0.6530 (t0) REVERT: F 400 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.7012 (t-90) REVERT: F 403 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6779 (ttp-170) REVERT: F 444 ARG cc_start: 0.7898 (ttp80) cc_final: 0.6765 (tpt90) REVERT: G 12 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6624 (mtp180) REVERT: G 17 ARG cc_start: 0.7221 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: G 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6895 (tp30) REVERT: G 79 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7757 (ttpt) REVERT: G 165 MET cc_start: 0.7307 (mtp) cc_final: 0.6986 (mtt) REVERT: G 184 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: G 213 GLU cc_start: 0.7107 (mp0) cc_final: 0.6709 (mp0) REVERT: G 224 LYS cc_start: 0.6250 (ttpp) cc_final: 0.5855 (pttp) REVERT: G 327 ASP cc_start: 0.5543 (OUTLIER) cc_final: 0.5329 (t70) REVERT: G 397 ASP cc_start: 0.6776 (m-30) cc_final: 0.6480 (t0) REVERT: G 400 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.7026 (t-90) REVERT: G 403 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6737 (ttp-170) REVERT: H 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6414 (tmt-80) REVERT: H 75 GLU cc_start: 0.7443 (tp30) cc_final: 0.6946 (tp30) REVERT: H 79 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: H 184 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: H 192 MET cc_start: 0.7352 (ppp) cc_final: 0.6994 (ppp) REVERT: H 213 GLU cc_start: 0.7024 (mp0) cc_final: 0.6624 (mp0) REVERT: H 224 LYS cc_start: 0.6336 (ttpp) cc_final: 0.5948 (pttp) REVERT: H 327 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.5366 (t70) REVERT: H 397 ASP cc_start: 0.6837 (m-30) cc_final: 0.6581 (t0) REVERT: H 400 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6909 (t-90) REVERT: H 403 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6720 (ttp-170) REVERT: H 444 ARG cc_start: 0.7934 (ttp80) cc_final: 0.6836 (tpt90) REVERT: H 483 GLU cc_start: 0.7228 (pt0) cc_final: 0.6966 (mt-10) REVERT: I 12 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6386 (mtp180) REVERT: I 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6435 (tmt-80) REVERT: I 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.6940 (tp30) REVERT: I 79 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7649 (mtmm) REVERT: I 184 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6425 (m-30) REVERT: I 192 MET cc_start: 0.7356 (ppp) cc_final: 0.6992 (ppp) REVERT: I 213 GLU cc_start: 0.6944 (mp0) cc_final: 0.6449 (mp0) REVERT: I 224 LYS cc_start: 0.6318 (ttpp) cc_final: 0.5822 (pttp) REVERT: I 397 ASP cc_start: 0.6726 (m-30) cc_final: 0.6438 (t0) REVERT: I 400 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6963 (t-90) REVERT: I 403 ARG cc_start: 0.7037 (ttm-80) cc_final: 0.6736 (ttp-170) REVERT: J 17 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6434 (tmt-80) REVERT: J 75 GLU cc_start: 0.7419 (tp30) cc_final: 0.7085 (tp30) REVERT: J 79 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7761 (ttpt) REVERT: J 165 MET cc_start: 0.7237 (mtp) cc_final: 0.6943 (mtt) REVERT: J 184 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6464 (m-30) REVERT: J 193 GLN cc_start: 0.7525 (pt0) cc_final: 0.7324 (pt0) REVERT: J 213 GLU cc_start: 0.6990 (mp0) cc_final: 0.6545 (mp0) REVERT: J 224 LYS cc_start: 0.6337 (ttpp) cc_final: 0.5886 (pttp) REVERT: J 327 ASP cc_start: 0.5553 (OUTLIER) cc_final: 0.5314 (t70) REVERT: J 397 ASP cc_start: 0.6882 (m-30) cc_final: 0.6578 (t0) REVERT: J 400 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6982 (t-90) REVERT: K 12 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6334 (mtp180) REVERT: K 17 ARG cc_start: 0.7199 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: K 75 GLU cc_start: 0.7414 (tp30) cc_final: 0.6945 (tp30) REVERT: K 165 MET cc_start: 0.7369 (mtm) cc_final: 0.7148 (mtt) REVERT: K 184 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6469 (m-30) REVERT: K 213 GLU cc_start: 0.7068 (mp0) cc_final: 0.6662 (mp0) REVERT: K 224 LYS cc_start: 0.6342 (ttpp) cc_final: 0.5854 (pttp) REVERT: K 266 MET cc_start: 0.6666 (mmm) cc_final: 0.6458 (mtm) REVERT: K 327 ASP cc_start: 0.5578 (OUTLIER) cc_final: 0.5341 (t70) REVERT: K 397 ASP cc_start: 0.6837 (m-30) cc_final: 0.6519 (t0) REVERT: K 400 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.7033 (t-90) REVERT: K 403 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.6769 (ttp-170) REVERT: L 12 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6358 (mtp180) REVERT: L 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6458 (tmt-80) REVERT: L 75 GLU cc_start: 0.7490 (tp30) cc_final: 0.7004 (tp30) REVERT: L 79 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7710 (ttpt) REVERT: L 184 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6453 (m-30) REVERT: L 190 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7247 (mm-30) REVERT: L 224 LYS cc_start: 0.6182 (ttpp) cc_final: 0.5860 (pttp) REVERT: L 327 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5359 (t70) REVERT: L 397 ASP cc_start: 0.6805 (m-30) cc_final: 0.6520 (t0) REVERT: L 400 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6980 (t-90) REVERT: M 12 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6299 (mtp180) REVERT: M 17 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6394 (tmt-80) REVERT: M 75 GLU cc_start: 0.7471 (tp30) cc_final: 0.6957 (tp30) REVERT: M 79 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7780 (ttpt) REVERT: M 184 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: M 224 LYS cc_start: 0.6247 (ttpp) cc_final: 0.5930 (pttp) REVERT: M 327 ASP cc_start: 0.5566 (OUTLIER) cc_final: 0.5364 (t70) REVERT: M 397 ASP cc_start: 0.6860 (m-30) cc_final: 0.6581 (t0) REVERT: M 400 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7039 (t-90) REVERT: M 403 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6707 (ttp-170) REVERT: M 444 ARG cc_start: 0.7891 (ttp80) cc_final: 0.6763 (tpt90) REVERT: M 483 GLU cc_start: 0.7200 (pt0) cc_final: 0.6973 (mt-10) REVERT: N 12 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6620 (mtp180) REVERT: N 17 ARG cc_start: 0.7220 (ttp-110) cc_final: 0.6462 (tmt-80) REVERT: N 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6887 (tp30) REVERT: N 79 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: N 165 MET cc_start: 0.7287 (mtp) cc_final: 0.7068 (mtt) REVERT: N 184 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: N 224 LYS cc_start: 0.6245 (ttpp) cc_final: 0.5809 (pttp) REVERT: N 327 ASP cc_start: 0.5539 (OUTLIER) cc_final: 0.5333 (t70) REVERT: N 397 ASP cc_start: 0.6760 (m-30) cc_final: 0.6469 (t0) REVERT: N 400 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.7054 (t-90) REVERT: N 403 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6750 (ttp-170) outliers start: 332 outliers final: 141 residues processed: 1130 average time/residue: 1.3872 time to fit residues: 2013.3565 Evaluate side-chains 1061 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 859 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 264 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain K residue 466 ASN Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 184 ASP Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 327 ASP Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 276 LYS Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 327 ASP Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 666 optimal weight: 3.9990 chunk 507 optimal weight: 6.9990 chunk 350 optimal weight: 0.0870 chunk 74 optimal weight: 30.0000 chunk 322 optimal weight: 0.8980 chunk 453 optimal weight: 20.0000 chunk 677 optimal weight: 0.7980 chunk 717 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 642 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN B 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN I 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 56042 Z= 0.173 Angle : 0.509 7.397 75712 Z= 0.267 Chirality : 0.041 0.149 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.469 50.107 7940 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.01 % Rotamer: Outliers : 5.77 % Allowed : 24.93 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.10), residues: 7462 helix: 2.33 (0.08), residues: 4228 sheet: -0.06 (0.15), residues: 1106 loop : -0.36 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 23 HIS 0.001 0.001 HIS G 400 PHE 0.008 0.001 PHE N 194 TYR 0.010 0.001 TYR C 505 ARG 0.004 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 904 time to evaluate : 4.617 Fit side-chains REVERT: A 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6402 (tmt-80) REVERT: A 75 GLU cc_start: 0.7401 (tp30) cc_final: 0.6895 (tp30) REVERT: A 79 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7785 (ttpt) REVERT: A 184 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6535 (m-30) REVERT: A 213 GLU cc_start: 0.7109 (mp0) cc_final: 0.6710 (mp0) REVERT: A 224 LYS cc_start: 0.6292 (ttpp) cc_final: 0.5883 (pttp) REVERT: A 327 ASP cc_start: 0.5556 (OUTLIER) cc_final: 0.5294 (t70) REVERT: A 397 ASP cc_start: 0.6860 (m-30) cc_final: 0.6583 (t0) REVERT: A 400 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6935 (t-90) REVERT: A 403 ARG cc_start: 0.7012 (ttm-80) cc_final: 0.6683 (ttp-170) REVERT: A 444 ARG cc_start: 0.7916 (ttp80) cc_final: 0.6808 (tpt90) REVERT: A 483 GLU cc_start: 0.7213 (pt0) cc_final: 0.6981 (mt-10) REVERT: B 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6421 (tmt-80) REVERT: B 75 GLU cc_start: 0.7432 (tp30) cc_final: 0.6931 (tp30) REVERT: B 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7727 (ttpt) REVERT: B 213 GLU cc_start: 0.6988 (mp0) cc_final: 0.6554 (mp0) REVERT: B 224 LYS cc_start: 0.6251 (ttpp) cc_final: 0.5863 (pttp) REVERT: B 327 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.5426 (t70) REVERT: B 400 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: B 403 ARG cc_start: 0.7101 (ttm-80) cc_final: 0.6763 (ttp-170) REVERT: C 12 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6314 (mtp180) REVERT: C 17 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6419 (tmt-80) REVERT: C 75 GLU cc_start: 0.7425 (tp30) cc_final: 0.7077 (tp30) REVERT: C 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7771 (ttpt) REVERT: C 165 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6995 (mtt) REVERT: C 213 GLU cc_start: 0.7036 (mp0) cc_final: 0.6628 (mp0) REVERT: C 224 LYS cc_start: 0.6270 (ttpp) cc_final: 0.5830 (pttp) REVERT: C 236 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5961 (mt) REVERT: C 400 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6971 (t-90) REVERT: D 12 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6299 (mtp180) REVERT: D 17 ARG cc_start: 0.7201 (ttp-110) cc_final: 0.6387 (tmt-80) REVERT: D 75 GLU cc_start: 0.7414 (tp30) cc_final: 0.6936 (tp30) REVERT: D 184 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: D 213 GLU cc_start: 0.7083 (mp0) cc_final: 0.6650 (mp0) REVERT: D 224 LYS cc_start: 0.6283 (ttpp) cc_final: 0.5813 (pttp) REVERT: D 321 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6948 (ttt90) REVERT: D 327 ASP cc_start: 0.5520 (OUTLIER) cc_final: 0.5306 (t70) REVERT: D 397 ASP cc_start: 0.6859 (m-30) cc_final: 0.6528 (t0) REVERT: D 400 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: D 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6738 (ttp-170) REVERT: E 12 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6367 (mtp180) REVERT: E 17 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6452 (tmt-80) REVERT: E 75 GLU cc_start: 0.7490 (tp30) cc_final: 0.7029 (tp30) REVERT: E 79 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7744 (ttpt) REVERT: E 213 GLU cc_start: 0.7043 (mp0) cc_final: 0.6584 (mp0) REVERT: E 224 LYS cc_start: 0.6134 (ttpp) cc_final: 0.5783 (pttp) REVERT: E 236 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5900 (mt) REVERT: E 283 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5814 (mpp80) REVERT: E 397 ASP cc_start: 0.6802 (m-30) cc_final: 0.6526 (t0) REVERT: E 400 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6959 (t-90) REVERT: F 12 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6262 (mtp180) REVERT: F 17 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: F 75 GLU cc_start: 0.7452 (tp30) cc_final: 0.6984 (tp30) REVERT: F 79 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7776 (ttpt) REVERT: F 213 GLU cc_start: 0.7109 (mp0) cc_final: 0.6620 (mp0) REVERT: F 224 LYS cc_start: 0.6326 (ttpp) cc_final: 0.5903 (pttp) REVERT: F 397 ASP cc_start: 0.6823 (m-30) cc_final: 0.6524 (t0) REVERT: F 400 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.7005 (t-90) REVERT: F 403 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6768 (ttp-170) REVERT: F 444 ARG cc_start: 0.7880 (ttp80) cc_final: 0.6707 (tpt90) REVERT: G 12 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6582 (mtp180) REVERT: G 17 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6451 (tmt-80) REVERT: G 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6893 (tp30) REVERT: G 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7760 (ttpt) REVERT: G 165 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: G 213 GLU cc_start: 0.7109 (mp0) cc_final: 0.6836 (mp0) REVERT: G 224 LYS cc_start: 0.6244 (ttpp) cc_final: 0.5829 (pttp) REVERT: G 236 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5948 (mt) REVERT: G 321 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6843 (ttt-90) REVERT: G 397 ASP cc_start: 0.6822 (m-30) cc_final: 0.6516 (t0) REVERT: G 400 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7060 (t-90) REVERT: G 403 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6739 (ttp-170) REVERT: H 17 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: H 75 GLU cc_start: 0.7402 (tp30) cc_final: 0.6895 (tp30) REVERT: H 79 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: H 184 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6535 (m-30) REVERT: H 213 GLU cc_start: 0.7111 (mp0) cc_final: 0.6712 (mp0) REVERT: H 224 LYS cc_start: 0.6286 (ttpp) cc_final: 0.5880 (pttp) REVERT: H 327 ASP cc_start: 0.5549 (OUTLIER) cc_final: 0.5291 (t70) REVERT: H 397 ASP cc_start: 0.6862 (m-30) cc_final: 0.6588 (t0) REVERT: H 400 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6926 (t-90) REVERT: H 403 ARG cc_start: 0.7014 (ttm-80) cc_final: 0.6683 (ttp-170) REVERT: H 444 ARG cc_start: 0.7915 (ttp80) cc_final: 0.6807 (tpt90) REVERT: H 483 GLU cc_start: 0.7216 (pt0) cc_final: 0.6985 (mt-10) REVERT: I 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6346 (mtp180) REVERT: I 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6431 (tmt-80) REVERT: I 75 GLU cc_start: 0.7432 (tp30) cc_final: 0.6928 (tp30) REVERT: I 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: I 224 LYS cc_start: 0.6283 (ttpp) cc_final: 0.5895 (pttp) REVERT: I 327 ASP cc_start: 0.5664 (OUTLIER) cc_final: 0.5415 (t70) REVERT: I 400 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6948 (t-90) REVERT: I 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6748 (ttp-170) REVERT: J 12 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6315 (mtp180) REVERT: J 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6420 (tmt-80) REVERT: J 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.7081 (tp30) REVERT: J 79 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7773 (ttpt) REVERT: J 165 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.7012 (mtt) REVERT: J 213 GLU cc_start: 0.7022 (mp0) cc_final: 0.6564 (mp0) REVERT: J 224 LYS cc_start: 0.6268 (ttpp) cc_final: 0.5839 (pttp) REVERT: J 236 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5956 (mt) REVERT: J 400 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6966 (t-90) REVERT: K 12 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6299 (mtp180) REVERT: K 17 ARG cc_start: 0.7191 (ttp-110) cc_final: 0.6381 (tmt-80) REVERT: K 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.6935 (tp30) REVERT: K 213 GLU cc_start: 0.7096 (mp0) cc_final: 0.6692 (mp0) REVERT: K 224 LYS cc_start: 0.6271 (ttpp) cc_final: 0.5791 (pttp) REVERT: K 327 ASP cc_start: 0.5541 (OUTLIER) cc_final: 0.5337 (t70) REVERT: K 397 ASP cc_start: 0.6854 (m-30) cc_final: 0.6522 (t0) REVERT: K 400 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7031 (t-90) REVERT: K 403 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6742 (ttp-170) REVERT: L 12 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6363 (mtp180) REVERT: L 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6447 (tmt-80) REVERT: L 75 GLU cc_start: 0.7470 (tp30) cc_final: 0.7007 (tp30) REVERT: L 79 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7744 (ttpt) REVERT: L 184 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6574 (m-30) REVERT: L 213 GLU cc_start: 0.7096 (mp0) cc_final: 0.6679 (mp0) REVERT: L 224 LYS cc_start: 0.6170 (ttpp) cc_final: 0.5886 (pttp) REVERT: L 236 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5910 (mt) REVERT: L 283 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5795 (mpp80) REVERT: L 397 ASP cc_start: 0.6807 (m-30) cc_final: 0.6525 (t0) REVERT: L 400 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6940 (t-90) REVERT: M 12 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6262 (mtp180) REVERT: M 17 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: M 75 GLU cc_start: 0.7457 (tp30) cc_final: 0.6986 (tp30) REVERT: M 79 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7770 (ttpt) REVERT: M 213 GLU cc_start: 0.7104 (mp0) cc_final: 0.6602 (mp0) REVERT: M 224 LYS cc_start: 0.6319 (ttpp) cc_final: 0.5876 (pttp) REVERT: M 397 ASP cc_start: 0.6817 (m-30) cc_final: 0.6532 (t0) REVERT: M 400 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: M 403 ARG cc_start: 0.7082 (ttm-80) cc_final: 0.6768 (ttp-170) REVERT: M 444 ARG cc_start: 0.7881 (ttp80) cc_final: 0.6704 (tpt90) REVERT: M 483 GLU cc_start: 0.7175 (pt0) cc_final: 0.6949 (mt-10) REVERT: N 12 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6585 (mtp180) REVERT: N 17 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6450 (tmt-80) REVERT: N 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6887 (tp30) REVERT: N 79 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7762 (ttpt) REVERT: N 165 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.7042 (mtt) REVERT: N 213 GLU cc_start: 0.7129 (mp0) cc_final: 0.6689 (mp0) REVERT: N 224 LYS cc_start: 0.6222 (ttpp) cc_final: 0.5718 (pttp) REVERT: N 236 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5967 (mt) REVERT: N 397 ASP cc_start: 0.6811 (m-30) cc_final: 0.6515 (t0) REVERT: N 400 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7060 (t-90) REVERT: N 403 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6725 (ttp-170) REVERT: T 26 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.4976 (t70) outliers start: 336 outliers final: 158 residues processed: 1141 average time/residue: 1.3051 time to fit residues: 1897.4619 Evaluate side-chains 1093 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 875 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 264 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 184 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 597 optimal weight: 0.2980 chunk 407 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 534 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 612 optimal weight: 5.9990 chunk 495 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 643 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN D 365 GLN E 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN K 365 GLN L 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56042 Z= 0.280 Angle : 0.565 8.085 75712 Z= 0.296 Chirality : 0.043 0.150 9142 Planarity : 0.004 0.031 9884 Dihedral : 4.750 59.787 7932 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.02 % Favored : 96.80 % Rotamer: Outliers : 7.19 % Allowed : 23.56 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 7462 helix: 2.12 (0.08), residues: 4228 sheet: 0.25 (0.19), residues: 756 loop : -0.76 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 2 18 HIS 0.004 0.002 HIS L 400 PHE 0.006 0.001 PHE G 194 TYR 0.013 0.001 TYR J 505 ARG 0.004 0.000 ARG J 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 886 time to evaluate : 4.688 Fit side-chains REVERT: A 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6415 (tmt-80) REVERT: A 75 GLU cc_start: 0.7470 (tp30) cc_final: 0.7035 (tp30) REVERT: A 79 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7778 (ttpt) REVERT: A 184 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: A 213 GLU cc_start: 0.7087 (mp0) cc_final: 0.6649 (mp0) REVERT: A 224 LYS cc_start: 0.6252 (ttpp) cc_final: 0.5845 (pttp) REVERT: A 306 MET cc_start: 0.4370 (mmp) cc_final: 0.4118 (mmp) REVERT: A 400 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6913 (t-90) REVERT: A 403 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6824 (mtt-85) REVERT: A 483 GLU cc_start: 0.7255 (pt0) cc_final: 0.7025 (mt-10) REVERT: B 17 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: B 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.6970 (tp30) REVERT: B 79 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7625 (mtmm) REVERT: B 184 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: B 224 LYS cc_start: 0.6277 (ttpp) cc_final: 0.5847 (pttp) REVERT: B 306 MET cc_start: 0.4403 (mmp) cc_final: 0.4192 (mmp) REVERT: B 400 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.6938 (t-90) REVERT: B 403 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6674 (ttp-170) REVERT: C 12 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6355 (mtp180) REVERT: C 17 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6482 (tmt-80) REVERT: C 75 GLU cc_start: 0.7463 (tp30) cc_final: 0.7016 (tp30) REVERT: C 79 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7720 (ttpt) REVERT: C 165 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6903 (mtt) REVERT: C 184 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: C 193 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: C 213 GLU cc_start: 0.6965 (mp0) cc_final: 0.6503 (mp0) REVERT: C 224 LYS cc_start: 0.6254 (ttpp) cc_final: 0.5823 (pttp) REVERT: C 236 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5961 (mt) REVERT: C 306 MET cc_start: 0.4439 (mmp) cc_final: 0.4203 (mmp) REVERT: C 400 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6960 (t-90) REVERT: D 12 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6298 (mtp180) REVERT: D 17 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6449 (tmt-80) REVERT: D 75 GLU cc_start: 0.7442 (tp30) cc_final: 0.7013 (tp30) REVERT: D 79 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: D 184 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6715 (m-30) REVERT: D 213 GLU cc_start: 0.7015 (mp0) cc_final: 0.6557 (mp0) REVERT: D 224 LYS cc_start: 0.6278 (ttpp) cc_final: 0.5792 (pttp) REVERT: D 306 MET cc_start: 0.4526 (mmp) cc_final: 0.4319 (mmp) REVERT: D 400 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6999 (t-90) REVERT: D 403 ARG cc_start: 0.7102 (ttm-80) cc_final: 0.6679 (ttp-110) REVERT: E 12 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6359 (mtp180) REVERT: E 17 ARG cc_start: 0.7302 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: E 43 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6659 (p90) REVERT: E 75 GLU cc_start: 0.7519 (tp30) cc_final: 0.7088 (tp30) REVERT: E 79 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7741 (ttpt) REVERT: E 213 GLU cc_start: 0.7050 (mp0) cc_final: 0.6595 (mp0) REVERT: E 224 LYS cc_start: 0.6136 (ttpp) cc_final: 0.5808 (pttp) REVERT: E 236 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5897 (mt) REVERT: E 283 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5793 (mpp80) REVERT: E 400 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6949 (t-90) REVERT: F 12 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: F 17 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6414 (tmt-80) REVERT: F 75 GLU cc_start: 0.7470 (tp30) cc_final: 0.6972 (tp30) REVERT: F 79 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7750 (ttpt) REVERT: F 184 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: F 213 GLU cc_start: 0.7092 (mp0) cc_final: 0.6535 (mp0) REVERT: F 224 LYS cc_start: 0.6295 (ttpp) cc_final: 0.6025 (pttp) REVERT: F 264 ASN cc_start: 0.5941 (OUTLIER) cc_final: 0.5631 (t0) REVERT: F 400 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: G 12 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6601 (mtp180) REVERT: G 17 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6489 (tmt-80) REVERT: G 75 GLU cc_start: 0.7481 (tp30) cc_final: 0.6949 (tp30) REVERT: G 79 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7714 (ttpt) REVERT: G 184 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: G 213 GLU cc_start: 0.7082 (mp0) cc_final: 0.6756 (mp0) REVERT: G 224 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5879 (pttp) REVERT: G 236 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5923 (mt) REVERT: G 306 MET cc_start: 0.4430 (mmp) cc_final: 0.4222 (mmp) REVERT: G 400 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.7041 (t-90) REVERT: G 403 ARG cc_start: 0.7097 (ttm-80) cc_final: 0.6714 (ttp-170) REVERT: H 17 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6412 (tmt-80) REVERT: H 75 GLU cc_start: 0.7470 (tp30) cc_final: 0.7036 (tp30) REVERT: H 79 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: H 184 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: H 213 GLU cc_start: 0.7086 (mp0) cc_final: 0.6647 (mp0) REVERT: H 224 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5840 (pttp) REVERT: H 306 MET cc_start: 0.4382 (mmp) cc_final: 0.4130 (mmp) REVERT: H 400 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6911 (t-90) REVERT: H 403 ARG cc_start: 0.7027 (ttm-80) cc_final: 0.6825 (mtt-85) REVERT: H 483 GLU cc_start: 0.7257 (pt0) cc_final: 0.7029 (mt-10) REVERT: I 12 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6234 (mtp180) REVERT: I 17 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6464 (tmt-80) REVERT: I 75 GLU cc_start: 0.7446 (tp30) cc_final: 0.6967 (tp30) REVERT: I 79 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7631 (mtmm) REVERT: I 184 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: I 224 LYS cc_start: 0.6295 (ttpp) cc_final: 0.5871 (pttp) REVERT: I 306 MET cc_start: 0.4381 (mmp) cc_final: 0.4171 (mmp) REVERT: I 321 ARG cc_start: 0.6864 (ttt90) cc_final: 0.6644 (ttt-90) REVERT: I 400 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6927 (t-90) REVERT: I 403 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6863 (mtt-85) REVERT: J 12 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.6354 (mtp180) REVERT: J 17 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6480 (tmt-80) REVERT: J 75 GLU cc_start: 0.7465 (tp30) cc_final: 0.7017 (tp30) REVERT: J 79 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7722 (ttpt) REVERT: J 165 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6901 (mtt) REVERT: J 184 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: J 213 GLU cc_start: 0.7000 (mp0) cc_final: 0.6534 (mp0) REVERT: J 224 LYS cc_start: 0.6253 (ttpp) cc_final: 0.5838 (pttp) REVERT: J 236 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5956 (mt) REVERT: J 306 MET cc_start: 0.4404 (mmp) cc_final: 0.4167 (mmp) REVERT: J 400 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.6979 (t-90) REVERT: K 12 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6299 (mtp180) REVERT: K 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6444 (tmt-80) REVERT: K 75 GLU cc_start: 0.7433 (tp30) cc_final: 0.7003 (tp30) REVERT: K 79 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7808 (mtpt) REVERT: K 213 GLU cc_start: 0.7047 (mp0) cc_final: 0.6583 (mp0) REVERT: K 224 LYS cc_start: 0.6279 (ttpp) cc_final: 0.5776 (pttp) REVERT: K 306 MET cc_start: 0.4524 (mmp) cc_final: 0.4314 (mmp) REVERT: K 400 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7011 (t-90) REVERT: K 403 ARG cc_start: 0.7110 (ttm-80) cc_final: 0.6678 (ttp-110) REVERT: L 12 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6355 (mtp180) REVERT: L 17 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: L 43 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6669 (p90) REVERT: L 75 GLU cc_start: 0.7514 (tp30) cc_final: 0.7029 (tp30) REVERT: L 79 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7740 (ttpt) REVERT: L 184 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: L 190 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7125 (mm-30) REVERT: L 193 GLN cc_start: 0.7416 (pt0) cc_final: 0.7124 (pt0) REVERT: L 213 GLU cc_start: 0.7106 (mp0) cc_final: 0.6660 (mp0) REVERT: L 224 LYS cc_start: 0.6112 (ttpp) cc_final: 0.5763 (pttp) REVERT: L 236 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5916 (mt) REVERT: L 283 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.5813 (mpp80) REVERT: L 400 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6956 (t-90) REVERT: M 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6266 (mtp180) REVERT: M 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: M 75 GLU cc_start: 0.7468 (tp30) cc_final: 0.6969 (tp30) REVERT: M 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7751 (ttpt) REVERT: M 184 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: M 213 GLU cc_start: 0.7102 (mp0) cc_final: 0.6549 (mp0) REVERT: M 224 LYS cc_start: 0.6314 (ttpp) cc_final: 0.5878 (pttp) REVERT: M 400 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: N 12 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6602 (mtp180) REVERT: N 17 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6486 (tmt-80) REVERT: N 75 GLU cc_start: 0.7473 (tp30) cc_final: 0.6947 (tp30) REVERT: N 79 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7713 (ttpt) REVERT: N 184 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: N 213 GLU cc_start: 0.7045 (mp0) cc_final: 0.6793 (mp0) REVERT: N 224 LYS cc_start: 0.6152 (ttpp) cc_final: 0.5814 (pttp) REVERT: N 236 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5936 (mt) REVERT: N 321 ARG cc_start: 0.6824 (ttt90) cc_final: 0.6536 (ttt-90) REVERT: N 400 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7017 (t-90) REVERT: N 403 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6719 (ttp-170) REVERT: R 26 HIS cc_start: 0.5292 (OUTLIER) cc_final: 0.5042 (t70) REVERT: S 26 HIS cc_start: 0.5431 (OUTLIER) cc_final: 0.5139 (t70) REVERT: Y 26 HIS cc_start: 0.5300 (OUTLIER) cc_final: 0.5035 (t70) outliers start: 419 outliers final: 216 residues processed: 1175 average time/residue: 1.2594 time to fit residues: 1900.3350 Evaluate side-chains 1156 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 872 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain K residue 466 ASN Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 43 PHE Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 184 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 241 optimal weight: 0.0980 chunk 645 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 421 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 717 optimal weight: 0.9990 chunk 595 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 237 optimal weight: 5.9990 chunk 376 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN E 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 56042 Z= 0.150 Angle : 0.502 7.823 75712 Z= 0.262 Chirality : 0.040 0.153 9142 Planarity : 0.003 0.030 9884 Dihedral : 4.589 59.985 7932 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 5.96 % Allowed : 24.93 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.10), residues: 7462 helix: 2.32 (0.08), residues: 4228 sheet: -0.04 (0.16), residues: 1106 loop : -0.37 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 1 18 HIS 0.002 0.001 HIS 1 26 PHE 0.008 0.001 PHE N 194 TYR 0.009 0.001 TYR C 505 ARG 0.004 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 888 time to evaluate : 4.625 Fit side-chains REVERT: A 17 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6394 (tmt-80) REVERT: A 75 GLU cc_start: 0.7457 (tp30) cc_final: 0.7008 (tp30) REVERT: A 79 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7747 (ttpt) REVERT: A 184 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: A 193 GLN cc_start: 0.7408 (pt0) cc_final: 0.7189 (pt0) REVERT: A 213 GLU cc_start: 0.7135 (mp0) cc_final: 0.6714 (mp0) REVERT: A 224 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5834 (pttp) REVERT: A 306 MET cc_start: 0.4377 (mmp) cc_final: 0.4163 (mmp) REVERT: A 400 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: A 403 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6702 (ttp-170) REVERT: A 444 ARG cc_start: 0.7904 (ttm110) cc_final: 0.6834 (tpt90) REVERT: A 483 GLU cc_start: 0.7195 (pt0) cc_final: 0.6966 (mt-10) REVERT: B 17 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: B 75 GLU cc_start: 0.7412 (tp30) cc_final: 0.6952 (tp30) REVERT: B 79 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7677 (ttpt) REVERT: B 224 LYS cc_start: 0.6307 (ttpp) cc_final: 0.5895 (pttp) REVERT: B 306 MET cc_start: 0.4466 (mmp) cc_final: 0.4217 (mmp) REVERT: B 400 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: B 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6686 (ttp-170) REVERT: C 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6433 (tmt-80) REVERT: C 75 GLU cc_start: 0.7439 (tp30) cc_final: 0.7103 (tp30) REVERT: C 79 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: C 165 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6881 (mtt) REVERT: C 213 GLU cc_start: 0.7037 (mp0) cc_final: 0.6585 (mp0) REVERT: C 224 LYS cc_start: 0.6192 (ttpp) cc_final: 0.5825 (pttp) REVERT: C 236 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5916 (mt) REVERT: C 306 MET cc_start: 0.4408 (mmp) cc_final: 0.4207 (mmp) REVERT: C 400 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6979 (t-90) REVERT: D 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: D 17 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: D 75 GLU cc_start: 0.7425 (tp30) cc_final: 0.6993 (tp30) REVERT: D 184 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: D 193 GLN cc_start: 0.7365 (pt0) cc_final: 0.7086 (pt0) REVERT: D 213 GLU cc_start: 0.7106 (mp0) cc_final: 0.6782 (mp0) REVERT: D 224 LYS cc_start: 0.6222 (ttpp) cc_final: 0.5926 (pttp) REVERT: D 321 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.7013 (ttt-90) REVERT: D 400 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7057 (t-90) REVERT: D 403 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6740 (ttp-170) REVERT: E 12 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.6344 (mtp180) REVERT: E 17 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.6449 (tmt-80) REVERT: E 75 GLU cc_start: 0.7483 (tp30) cc_final: 0.7043 (tp30) REVERT: E 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7726 (ttpt) REVERT: E 193 GLN cc_start: 0.7429 (pt0) cc_final: 0.7150 (pt0) REVERT: E 213 GLU cc_start: 0.7099 (mp0) cc_final: 0.6664 (mp0) REVERT: E 224 LYS cc_start: 0.6148 (ttpp) cc_final: 0.5865 (pttp) REVERT: E 236 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5889 (mt) REVERT: E 400 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.7005 (t-90) REVERT: F 12 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6256 (mtp180) REVERT: F 17 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6391 (tmt-80) REVERT: F 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6962 (tp30) REVERT: F 79 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7737 (ttpt) REVERT: F 213 GLU cc_start: 0.7142 (mp0) cc_final: 0.6578 (mp0) REVERT: F 224 LYS cc_start: 0.6369 (ttpp) cc_final: 0.6054 (pttp) REVERT: F 400 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6986 (t-90) REVERT: G 17 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: G 75 GLU cc_start: 0.7471 (tp30) cc_final: 0.6921 (tp30) REVERT: G 79 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: G 213 GLU cc_start: 0.7149 (mp0) cc_final: 0.6709 (mp0) REVERT: G 224 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5811 (pttp) REVERT: G 236 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5929 (mt) REVERT: G 400 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: G 403 ARG cc_start: 0.7076 (ttm-80) cc_final: 0.6694 (ttp-170) REVERT: H 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6395 (tmt-80) REVERT: H 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7006 (tp30) REVERT: H 79 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: H 184 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: H 193 GLN cc_start: 0.7408 (pt0) cc_final: 0.7191 (pt0) REVERT: H 213 GLU cc_start: 0.7135 (mp0) cc_final: 0.6713 (mp0) REVERT: H 224 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5838 (pttp) REVERT: H 306 MET cc_start: 0.4390 (mmp) cc_final: 0.4172 (mmp) REVERT: H 400 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6899 (t-90) REVERT: H 403 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6700 (ttp-170) REVERT: H 444 ARG cc_start: 0.7905 (ttm110) cc_final: 0.6835 (tpt90) REVERT: H 483 GLU cc_start: 0.7198 (pt0) cc_final: 0.6969 (mt-10) REVERT: I 12 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6300 (mtp180) REVERT: I 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6427 (tmt-80) REVERT: I 75 GLU cc_start: 0.7413 (tp30) cc_final: 0.6949 (tp30) REVERT: I 79 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7674 (ttpt) REVERT: I 224 LYS cc_start: 0.6301 (ttpp) cc_final: 0.5893 (pttp) REVERT: I 306 MET cc_start: 0.4453 (mmp) cc_final: 0.4202 (mmp) REVERT: I 400 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6959 (t-90) REVERT: I 403 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6675 (ttp-170) REVERT: J 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6445 (tmt-80) REVERT: J 75 GLU cc_start: 0.7439 (tp30) cc_final: 0.7101 (tp30) REVERT: J 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7753 (ttpt) REVERT: J 165 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: J 213 GLU cc_start: 0.7058 (mp0) cc_final: 0.6619 (mp0) REVERT: J 224 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5862 (pttp) REVERT: J 236 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5920 (mt) REVERT: J 306 MET cc_start: 0.4386 (mmp) cc_final: 0.4185 (mmp) REVERT: J 400 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6954 (t-90) REVERT: K 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6272 (mtp180) REVERT: K 17 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.6394 (tmt-80) REVERT: K 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.6982 (tp30) REVERT: K 193 GLN cc_start: 0.7370 (pt0) cc_final: 0.7085 (pt0) REVERT: K 213 GLU cc_start: 0.7142 (mp0) cc_final: 0.6653 (mp0) REVERT: K 224 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5927 (pttp) REVERT: K 400 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: K 403 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6717 (ttp-170) REVERT: L 12 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6340 (mtp180) REVERT: L 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6445 (tmt-80) REVERT: L 75 GLU cc_start: 0.7481 (tp30) cc_final: 0.7041 (tp30) REVERT: L 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7725 (ttpt) REVERT: L 193 GLN cc_start: 0.7390 (pt0) cc_final: 0.7145 (pt0) REVERT: L 213 GLU cc_start: 0.7125 (mp0) cc_final: 0.6691 (mp0) REVERT: L 224 LYS cc_start: 0.6131 (ttpp) cc_final: 0.5854 (pttp) REVERT: L 236 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5894 (mt) REVERT: L 400 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: M 12 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6247 (mtp180) REVERT: M 17 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: M 75 GLU cc_start: 0.7434 (tp30) cc_final: 0.6962 (tp30) REVERT: M 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7738 (ttpt) REVERT: M 213 GLU cc_start: 0.7142 (mp0) cc_final: 0.6564 (mp0) REVERT: M 224 LYS cc_start: 0.6359 (ttpp) cc_final: 0.6041 (pttp) REVERT: M 264 ASN cc_start: 0.5962 (OUTLIER) cc_final: 0.5649 (t0) REVERT: M 400 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6989 (t-90) REVERT: N 17 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6461 (tmt-80) REVERT: N 75 GLU cc_start: 0.7467 (tp30) cc_final: 0.6936 (tp30) REVERT: N 79 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: N 213 GLU cc_start: 0.7092 (mp0) cc_final: 0.6803 (mp0) REVERT: N 224 LYS cc_start: 0.6187 (ttpp) cc_final: 0.5795 (pttp) REVERT: N 236 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5962 (mt) REVERT: N 321 ARG cc_start: 0.6748 (ttt90) cc_final: 0.6468 (ttt-90) REVERT: N 400 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7072 (t-90) REVERT: N 403 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6695 (ttp-170) REVERT: R 26 HIS cc_start: 0.5224 (OUTLIER) cc_final: 0.5007 (t70) REVERT: S 26 HIS cc_start: 0.5374 (OUTLIER) cc_final: 0.5098 (t70) REVERT: T 26 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.5041 (t70) REVERT: Y 26 HIS cc_start: 0.5212 (OUTLIER) cc_final: 0.4968 (t70) outliers start: 347 outliers final: 177 residues processed: 1152 average time/residue: 1.2264 time to fit residues: 1815.1186 Evaluate side-chains 1107 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 881 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 320 LYS Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 692 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 409 optimal weight: 0.8980 chunk 524 optimal weight: 0.6980 chunk 406 optimal weight: 0.4980 chunk 604 optimal weight: 1.9990 chunk 400 optimal weight: 10.0000 chunk 715 optimal weight: 3.9990 chunk 447 optimal weight: 0.6980 chunk 436 optimal weight: 0.7980 chunk 330 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 56042 Z= 0.140 Angle : 0.499 8.217 75712 Z= 0.258 Chirality : 0.041 0.177 9142 Planarity : 0.003 0.030 9884 Dihedral : 4.376 57.241 7927 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.57 % Favored : 97.24 % Rotamer: Outliers : 5.70 % Allowed : 25.27 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.10), residues: 7462 helix: 2.43 (0.08), residues: 4228 sheet: 0.05 (0.16), residues: 1106 loop : -0.36 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP X 23 HIS 0.002 0.001 HIS 1 26 PHE 0.008 0.001 PHE G 194 TYR 0.009 0.001 TYR J 505 ARG 0.005 0.000 ARG M 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 901 time to evaluate : 4.534 Fit side-chains REVERT: A 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6411 (tmt-80) REVERT: A 75 GLU cc_start: 0.7426 (tp30) cc_final: 0.7164 (tp30) REVERT: A 79 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7829 (ttpt) REVERT: A 213 GLU cc_start: 0.7110 (mp0) cc_final: 0.6663 (mp0) REVERT: A 224 LYS cc_start: 0.6187 (ttpp) cc_final: 0.5933 (pttp) REVERT: A 400 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: A 403 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6704 (ttp-170) REVERT: A 444 ARG cc_start: 0.7929 (ttm110) cc_final: 0.6795 (tpt90) REVERT: A 483 GLU cc_start: 0.7205 (pt0) cc_final: 0.7000 (mt-10) REVERT: B 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6419 (tmt-80) REVERT: B 75 GLU cc_start: 0.7394 (tp30) cc_final: 0.6941 (tp30) REVERT: B 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7706 (ttpt) REVERT: B 224 LYS cc_start: 0.6310 (ttpp) cc_final: 0.5919 (pttp) REVERT: B 321 ARG cc_start: 0.6610 (ttt90) cc_final: 0.6353 (ttt-90) REVERT: B 400 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: B 403 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6669 (ttp-170) REVERT: B 444 ARG cc_start: 0.7993 (ttm170) cc_final: 0.6778 (tpt90) REVERT: C 17 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6438 (tmt-80) REVERT: C 75 GLU cc_start: 0.7422 (tp30) cc_final: 0.7155 (tp30) REVERT: C 165 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6850 (mtt) REVERT: C 224 LYS cc_start: 0.6283 (ttpp) cc_final: 0.5888 (pttp) REVERT: C 236 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5906 (mt) REVERT: C 283 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5935 (mpp80) REVERT: C 306 MET cc_start: 0.4367 (mmp) cc_final: 0.4134 (mmp) REVERT: C 400 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.7012 (t-90) REVERT: C 444 ARG cc_start: 0.7964 (ttm110) cc_final: 0.6794 (tpt90) REVERT: D 12 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6276 (mtp180) REVERT: D 17 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6405 (tmt-80) REVERT: D 75 GLU cc_start: 0.7410 (tp30) cc_final: 0.6976 (tp30) REVERT: D 193 GLN cc_start: 0.7387 (pt0) cc_final: 0.7116 (pt0) REVERT: D 213 GLU cc_start: 0.7112 (mp0) cc_final: 0.6773 (mp0) REVERT: D 224 LYS cc_start: 0.6280 (ttpp) cc_final: 0.5860 (pttp) REVERT: D 400 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: D 403 ARG cc_start: 0.7102 (ttm-80) cc_final: 0.6699 (ttp-170) REVERT: D 444 ARG cc_start: 0.7947 (ttm170) cc_final: 0.6713 (tpt90) REVERT: E 12 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6324 (mtp180) REVERT: E 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: E 75 GLU cc_start: 0.7457 (tp30) cc_final: 0.7010 (tp30) REVERT: E 79 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7814 (ttpt) REVERT: E 193 GLN cc_start: 0.7419 (pt0) cc_final: 0.7160 (pt0) REVERT: E 213 GLU cc_start: 0.7113 (mp0) cc_final: 0.6652 (mp0) REVERT: E 224 LYS cc_start: 0.6233 (ttpp) cc_final: 0.5930 (pttp) REVERT: E 236 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5895 (mt) REVERT: E 400 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: F 12 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6241 (mtp180) REVERT: F 17 ARG cc_start: 0.7211 (ttp-110) cc_final: 0.6390 (tmt-80) REVERT: F 75 GLU cc_start: 0.7423 (tp30) cc_final: 0.6903 (tp30) REVERT: F 79 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7803 (ttpt) REVERT: F 213 GLU cc_start: 0.7141 (mp0) cc_final: 0.6595 (mp0) REVERT: F 224 LYS cc_start: 0.6397 (ttpp) cc_final: 0.6093 (pttp) REVERT: F 264 ASN cc_start: 0.5933 (OUTLIER) cc_final: 0.5613 (t0) REVERT: F 400 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.7016 (t-90) REVERT: F 444 ARG cc_start: 0.7913 (ttm110) cc_final: 0.6738 (tpt90) REVERT: G 12 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6550 (mtp180) REVERT: G 17 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.6442 (tmt-80) REVERT: G 58 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7455 (mm-30) REVERT: G 75 GLU cc_start: 0.7443 (tp30) cc_final: 0.6909 (tp30) REVERT: G 79 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7734 (ttpt) REVERT: G 224 LYS cc_start: 0.6314 (ttpp) cc_final: 0.5853 (pttp) REVERT: G 236 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5967 (mt) REVERT: G 306 MET cc_start: 0.4186 (mmp) cc_final: 0.3866 (mmp) REVERT: G 400 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: G 403 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: G 444 ARG cc_start: 0.7977 (ttm170) cc_final: 0.6772 (tpt90) REVERT: H 17 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6410 (tmt-80) REVERT: H 75 GLU cc_start: 0.7430 (tp30) cc_final: 0.7166 (tp30) REVERT: H 79 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7828 (ttpt) REVERT: H 213 GLU cc_start: 0.7108 (mp0) cc_final: 0.6662 (mp0) REVERT: H 224 LYS cc_start: 0.6183 (ttpp) cc_final: 0.5931 (pttp) REVERT: H 400 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6927 (t-90) REVERT: H 403 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6703 (ttp-170) REVERT: H 444 ARG cc_start: 0.7927 (ttm110) cc_final: 0.6794 (tpt90) REVERT: H 483 GLU cc_start: 0.7207 (pt0) cc_final: 0.7005 (mt-10) REVERT: I 12 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6319 (mtp180) REVERT: I 17 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6417 (tmt-80) REVERT: I 75 GLU cc_start: 0.7404 (tp30) cc_final: 0.6934 (tp30) REVERT: I 79 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7704 (ttpt) REVERT: I 224 LYS cc_start: 0.6278 (ttpp) cc_final: 0.5951 (pttp) REVERT: I 400 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6973 (t-90) REVERT: I 403 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6660 (ttp-170) REVERT: I 444 ARG cc_start: 0.7990 (ttm170) cc_final: 0.6765 (tpt90) REVERT: J 17 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6435 (tmt-80) REVERT: J 75 GLU cc_start: 0.7422 (tp30) cc_final: 0.7154 (tp30) REVERT: J 165 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6844 (mtt) REVERT: J 213 GLU cc_start: 0.7065 (mp0) cc_final: 0.6599 (mp0) REVERT: J 224 LYS cc_start: 0.6280 (ttpp) cc_final: 0.5904 (pttp) REVERT: J 236 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5904 (mt) REVERT: J 283 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5937 (mpp80) REVERT: J 306 MET cc_start: 0.4345 (mmp) cc_final: 0.4088 (mmp) REVERT: J 400 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: J 444 ARG cc_start: 0.7963 (ttm110) cc_final: 0.6794 (tpt90) REVERT: K 12 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6272 (mtp180) REVERT: K 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6400 (tmt-80) REVERT: K 75 GLU cc_start: 0.7413 (tp30) cc_final: 0.6978 (tp30) REVERT: K 193 GLN cc_start: 0.7376 (pt0) cc_final: 0.7103 (pt0) REVERT: K 213 GLU cc_start: 0.7085 (mp0) cc_final: 0.6793 (mp0) REVERT: K 224 LYS cc_start: 0.6285 (ttpp) cc_final: 0.5863 (pttp) REVERT: K 321 ARG cc_start: 0.6820 (ttt90) cc_final: 0.6564 (ttt-90) REVERT: K 400 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.7057 (t-90) REVERT: K 403 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6707 (ttp-170) REVERT: K 444 ARG cc_start: 0.7947 (ttm170) cc_final: 0.6713 (tpt90) REVERT: L 12 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6310 (mtp180) REVERT: L 17 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6425 (tmt-80) REVERT: L 75 GLU cc_start: 0.7439 (tp30) cc_final: 0.6994 (tp30) REVERT: L 79 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7817 (ttpt) REVERT: L 193 GLN cc_start: 0.7428 (pt0) cc_final: 0.7167 (pt0) REVERT: L 213 GLU cc_start: 0.7139 (mp0) cc_final: 0.6674 (mp0) REVERT: L 224 LYS cc_start: 0.6196 (ttpp) cc_final: 0.5878 (pttp) REVERT: L 236 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5877 (mt) REVERT: L 400 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.7014 (t-90) REVERT: M 12 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6244 (mtp180) REVERT: M 17 ARG cc_start: 0.7212 (ttp-110) cc_final: 0.6387 (tmt-80) REVERT: M 75 GLU cc_start: 0.7423 (tp30) cc_final: 0.6902 (tp30) REVERT: M 79 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7806 (ttpt) REVERT: M 213 GLU cc_start: 0.7147 (mp0) cc_final: 0.6602 (mp0) REVERT: M 224 LYS cc_start: 0.6418 (ttpp) cc_final: 0.6091 (pttp) REVERT: M 264 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5661 (t0) REVERT: M 400 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: M 444 ARG cc_start: 0.7911 (ttm110) cc_final: 0.6730 (tpt90) REVERT: N 12 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6550 (mtp180) REVERT: N 17 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: N 58 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7455 (mm-30) REVERT: N 75 GLU cc_start: 0.7440 (tp30) cc_final: 0.6907 (tp30) REVERT: N 79 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: N 224 LYS cc_start: 0.6225 (ttpp) cc_final: 0.5911 (pttp) REVERT: N 236 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5959 (mt) REVERT: N 321 ARG cc_start: 0.6763 (ttt90) cc_final: 0.6486 (ttt-90) REVERT: N 400 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: N 403 ARG cc_start: 0.7104 (ttm-80) cc_final: 0.6715 (ttp-170) REVERT: N 444 ARG cc_start: 0.7975 (ttm170) cc_final: 0.6754 (tpt90) REVERT: R 26 HIS cc_start: 0.5173 (OUTLIER) cc_final: 0.4967 (t70) REVERT: S 26 HIS cc_start: 0.5319 (OUTLIER) cc_final: 0.5033 (t70) REVERT: T 26 HIS cc_start: 0.5276 (OUTLIER) cc_final: 0.4987 (t70) outliers start: 332 outliers final: 164 residues processed: 1134 average time/residue: 1.2415 time to fit residues: 1805.1970 Evaluate side-chains 1099 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 887 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 320 LYS Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain W residue 26 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 442 optimal weight: 3.9990 chunk 285 optimal weight: 30.0000 chunk 427 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 454 optimal weight: 0.9980 chunk 487 optimal weight: 8.9990 chunk 353 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 562 optimal weight: 0.0670 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 56042 Z= 0.150 Angle : 0.501 8.323 75712 Z= 0.259 Chirality : 0.041 0.162 9142 Planarity : 0.003 0.031 9884 Dihedral : 4.281 54.154 7923 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.19 % Rotamer: Outliers : 5.05 % Allowed : 26.12 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.10), residues: 7462 helix: 2.46 (0.08), residues: 4228 sheet: 0.08 (0.16), residues: 1106 loop : -0.40 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 1 23 HIS 0.001 0.001 HIS 1 26 PHE 0.008 0.001 PHE G 194 TYR 0.007 0.001 TYR F 505 ARG 0.006 0.000 ARG L 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 882 time to evaluate : 4.540 Fit side-chains REVERT: A 17 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: A 75 GLU cc_start: 0.7411 (tp30) cc_final: 0.7150 (tp30) REVERT: A 79 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7859 (ttpt) REVERT: A 213 GLU cc_start: 0.7122 (mp0) cc_final: 0.6671 (mp0) REVERT: A 224 LYS cc_start: 0.6220 (ttpp) cc_final: 0.5954 (pttp) REVERT: A 400 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6933 (t-90) REVERT: A 403 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6704 (ttp-170) REVERT: A 444 ARG cc_start: 0.7954 (ttm110) cc_final: 0.6815 (tpt90) REVERT: A 483 GLU cc_start: 0.7209 (pt0) cc_final: 0.7003 (mt-10) REVERT: B 17 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: B 75 GLU cc_start: 0.7394 (tp30) cc_final: 0.6933 (tp30) REVERT: B 79 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: B 224 LYS cc_start: 0.6343 (ttpp) cc_final: 0.5940 (pttp) REVERT: B 321 ARG cc_start: 0.6655 (ttt90) cc_final: 0.6407 (ttt-90) REVERT: B 388 MET cc_start: 0.5973 (tpt) cc_final: 0.5730 (tpp) REVERT: B 400 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: B 403 ARG cc_start: 0.7076 (ttm-80) cc_final: 0.6666 (ttp-170) REVERT: B 444 ARG cc_start: 0.7988 (ttm170) cc_final: 0.6751 (tpt90) REVERT: C 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6444 (tmt-80) REVERT: C 75 GLU cc_start: 0.7411 (tp30) cc_final: 0.7162 (tp30) REVERT: C 165 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6857 (mtt) REVERT: C 224 LYS cc_start: 0.6254 (ttpp) cc_final: 0.5894 (pttp) REVERT: C 236 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5902 (mt) REVERT: C 283 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5931 (mpp80) REVERT: C 306 MET cc_start: 0.4409 (mmp) cc_final: 0.4147 (mmp) REVERT: C 400 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.7014 (t-90) REVERT: C 444 ARG cc_start: 0.7970 (ttm110) cc_final: 0.6793 (tpt90) REVERT: D 12 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: D 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: D 75 GLU cc_start: 0.7417 (tp30) cc_final: 0.6976 (tp30) REVERT: D 193 GLN cc_start: 0.7350 (pt0) cc_final: 0.7085 (pt0) REVERT: D 213 GLU cc_start: 0.7159 (mp0) cc_final: 0.6676 (mp0) REVERT: D 224 LYS cc_start: 0.6258 (ttpp) cc_final: 0.5877 (pttp) REVERT: D 400 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: D 403 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6688 (ttp-170) REVERT: D 444 ARG cc_start: 0.7966 (ttm170) cc_final: 0.6743 (tpt90) REVERT: E 12 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6341 (mtp180) REVERT: E 17 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6434 (tmt-80) REVERT: E 75 GLU cc_start: 0.7444 (tp30) cc_final: 0.7027 (tp30) REVERT: E 79 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7804 (ttpt) REVERT: E 193 GLN cc_start: 0.7427 (pt0) cc_final: 0.7184 (pt0) REVERT: E 224 LYS cc_start: 0.6287 (ttpp) cc_final: 0.5949 (pttp) REVERT: E 236 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5890 (mt) REVERT: E 283 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5851 (mpp80) REVERT: E 400 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7004 (t-90) REVERT: F 12 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6250 (mtp180) REVERT: F 17 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6389 (tmt-80) REVERT: F 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6912 (tp30) REVERT: F 79 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7819 (ttpt) REVERT: F 224 LYS cc_start: 0.6433 (ttpp) cc_final: 0.6135 (pttp) REVERT: F 264 ASN cc_start: 0.5904 (OUTLIER) cc_final: 0.5649 (t0) REVERT: F 400 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.7029 (t-90) REVERT: F 444 ARG cc_start: 0.7912 (ttm110) cc_final: 0.6734 (tpt90) REVERT: G 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6449 (tmt-80) REVERT: G 58 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7439 (mm-30) REVERT: G 75 GLU cc_start: 0.7443 (tp30) cc_final: 0.6903 (tp30) REVERT: G 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7757 (ttpt) REVERT: G 224 LYS cc_start: 0.6277 (ttpp) cc_final: 0.5874 (pttp) REVERT: G 236 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5984 (mt) REVERT: G 306 MET cc_start: 0.4269 (mmp) cc_final: 0.3896 (mmp) REVERT: G 400 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.7051 (t-90) REVERT: G 403 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6699 (ttp-170) REVERT: G 444 ARG cc_start: 0.7994 (ttm170) cc_final: 0.6767 (tpt90) REVERT: H 17 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: H 75 GLU cc_start: 0.7413 (tp30) cc_final: 0.7153 (tp30) REVERT: H 79 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7858 (ttpt) REVERT: H 213 GLU cc_start: 0.7119 (mp0) cc_final: 0.6667 (mp0) REVERT: H 224 LYS cc_start: 0.6220 (ttpp) cc_final: 0.5951 (pttp) REVERT: H 400 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6930 (t-90) REVERT: H 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6704 (ttp-170) REVERT: H 444 ARG cc_start: 0.7952 (ttm110) cc_final: 0.6813 (tpt90) REVERT: H 483 GLU cc_start: 0.7212 (pt0) cc_final: 0.7008 (mt-10) REVERT: I 12 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6325 (mtp180) REVERT: I 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6426 (tmt-80) REVERT: I 75 GLU cc_start: 0.7393 (tp30) cc_final: 0.6930 (tp30) REVERT: I 79 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: I 224 LYS cc_start: 0.6350 (ttpp) cc_final: 0.5968 (pttp) REVERT: I 400 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: I 403 ARG cc_start: 0.7065 (ttm-80) cc_final: 0.6655 (ttp-170) REVERT: I 444 ARG cc_start: 0.7983 (ttm170) cc_final: 0.6771 (tpt90) REVERT: J 17 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: J 75 GLU cc_start: 0.7411 (tp30) cc_final: 0.7161 (tp30) REVERT: J 165 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6865 (mtt) REVERT: J 193 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: J 224 LYS cc_start: 0.6263 (ttpp) cc_final: 0.5894 (pttp) REVERT: J 236 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5877 (mt) REVERT: J 283 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5939 (mpp80) REVERT: J 306 MET cc_start: 0.4389 (mmp) cc_final: 0.4132 (mmp) REVERT: J 400 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.7011 (t-90) REVERT: J 444 ARG cc_start: 0.7968 (ttm110) cc_final: 0.6793 (tpt90) REVERT: K 12 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: K 17 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: K 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.6988 (tp30) REVERT: K 193 GLN cc_start: 0.7351 (pt0) cc_final: 0.7080 (pt0) REVERT: K 213 GLU cc_start: 0.7141 (mp0) cc_final: 0.6836 (mp0) REVERT: K 224 LYS cc_start: 0.6237 (ttpp) cc_final: 0.5860 (pttp) REVERT: K 321 ARG cc_start: 0.6815 (ttt90) cc_final: 0.6573 (ttt-90) REVERT: K 400 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.7068 (t-90) REVERT: K 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6692 (ttp-170) REVERT: K 444 ARG cc_start: 0.7967 (ttm170) cc_final: 0.6744 (tpt90) REVERT: L 12 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6337 (mtp180) REVERT: L 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: L 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.7017 (tp30) REVERT: L 79 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7812 (ttpt) REVERT: L 193 GLN cc_start: 0.7465 (pt0) cc_final: 0.7244 (pt0) REVERT: L 224 LYS cc_start: 0.6210 (ttpp) cc_final: 0.5859 (pttp) REVERT: L 236 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5904 (mt) REVERT: L 283 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5852 (mpp80) REVERT: L 400 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: M 12 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6255 (mtp180) REVERT: M 17 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6391 (tmt-80) REVERT: M 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.6898 (tp30) REVERT: M 79 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7823 (ttpt) REVERT: M 224 LYS cc_start: 0.6375 (ttpp) cc_final: 0.6104 (pttp) REVERT: M 264 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.5655 (t0) REVERT: M 400 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.7032 (t-90) REVERT: M 444 ARG cc_start: 0.7914 (ttm110) cc_final: 0.6728 (tpt90) REVERT: N 12 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6553 (mtp180) REVERT: N 17 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6448 (tmt-80) REVERT: N 58 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7439 (mm-30) REVERT: N 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6899 (tp30) REVERT: N 79 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7758 (ttpt) REVERT: N 224 LYS cc_start: 0.6262 (ttpp) cc_final: 0.5926 (pttp) REVERT: N 236 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5984 (mt) REVERT: N 321 ARG cc_start: 0.6722 (ttt90) cc_final: 0.6484 (ttt-90) REVERT: N 400 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.7066 (t-90) REVERT: N 403 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6718 (ttp-170) REVERT: N 444 ARG cc_start: 0.7975 (ttm170) cc_final: 0.6753 (tpt90) REVERT: S 26 HIS cc_start: 0.5271 (OUTLIER) cc_final: 0.4993 (t70) REVERT: T 26 HIS cc_start: 0.5255 (OUTLIER) cc_final: 0.4956 (t70) outliers start: 294 outliers final: 163 residues processed: 1092 average time/residue: 1.2814 time to fit residues: 1795.3058 Evaluate side-chains 1085 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 873 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 193 GLN Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 320 LYS Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain W residue 26 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 650 optimal weight: 9.9990 chunk 685 optimal weight: 2.9990 chunk 625 optimal weight: 0.8980 chunk 666 optimal weight: 0.9980 chunk 684 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 523 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 602 optimal weight: 7.9990 chunk 630 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN G 318 GLN G 365 GLN H 365 GLN J 365 GLN K 365 GLN L 365 GLN M 365 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 56042 Z= 0.240 Angle : 0.554 10.884 75712 Z= 0.286 Chirality : 0.042 0.165 9142 Planarity : 0.003 0.032 9884 Dihedral : 4.156 48.959 7917 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 4.76 % Allowed : 26.10 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 7462 helix: 2.29 (0.08), residues: 4228 sheet: -0.04 (0.16), residues: 1106 loop : -0.55 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 23 HIS 0.003 0.001 HIS D 400 PHE 0.007 0.001 PHE N 194 TYR 0.009 0.001 TYR J 505 ARG 0.004 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 881 time to evaluate : 4.588 Fit side-chains REVERT: A 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6405 (tmt-80) REVERT: A 75 GLU cc_start: 0.7461 (tp30) cc_final: 0.7011 (tp30) REVERT: A 79 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7829 (ttpt) REVERT: A 213 GLU cc_start: 0.7164 (mp0) cc_final: 0.6711 (mp0) REVERT: A 224 LYS cc_start: 0.6241 (ttpp) cc_final: 0.5910 (pttp) REVERT: A 288 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6614 (mp) REVERT: A 400 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6916 (t-90) REVERT: A 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6883 (mtt-85) REVERT: B 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: B 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6977 (tp30) REVERT: B 79 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: B 224 LYS cc_start: 0.6314 (ttpp) cc_final: 0.5954 (pttp) REVERT: B 321 ARG cc_start: 0.6645 (ttt90) cc_final: 0.6421 (ttt-90) REVERT: B 400 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6977 (t-90) REVERT: B 403 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6652 (ttp-170) REVERT: C 17 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6471 (tmt-80) REVERT: C 75 GLU cc_start: 0.7457 (tp30) cc_final: 0.7142 (tp30) REVERT: C 165 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: C 224 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5863 (pttp) REVERT: C 236 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5938 (mt) REVERT: C 283 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5910 (mpp80) REVERT: C 306 MET cc_start: 0.4459 (mmp) cc_final: 0.4132 (mmp) REVERT: C 400 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6992 (t-90) REVERT: D 12 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6304 (mtp180) REVERT: D 17 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.6438 (tmt-80) REVERT: D 75 GLU cc_start: 0.7461 (tp30) cc_final: 0.7019 (tp30) REVERT: D 193 GLN cc_start: 0.7354 (pt0) cc_final: 0.7082 (pt0) REVERT: D 213 GLU cc_start: 0.7138 (mp0) cc_final: 0.6643 (mp0) REVERT: D 224 LYS cc_start: 0.6243 (ttpp) cc_final: 0.5847 (pttp) REVERT: D 400 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: D 403 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6638 (ttp-110) REVERT: E 12 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6349 (mtp180) REVERT: E 17 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6470 (tmt-80) REVERT: E 75 GLU cc_start: 0.7507 (tp30) cc_final: 0.7065 (tp30) REVERT: E 79 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: E 193 GLN cc_start: 0.7433 (pt0) cc_final: 0.7190 (pt0) REVERT: E 224 LYS cc_start: 0.6227 (ttpp) cc_final: 0.5877 (pttp) REVERT: E 236 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5884 (mt) REVERT: E 283 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5837 (mpp80) REVERT: E 400 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6979 (t-90) REVERT: F 12 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6277 (mtp180) REVERT: F 17 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6399 (tmt-80) REVERT: F 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6979 (tp30) REVERT: F 79 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7783 (ttpt) REVERT: F 224 LYS cc_start: 0.6419 (ttpp) cc_final: 0.6104 (pttp) REVERT: F 264 ASN cc_start: 0.5919 (OUTLIER) cc_final: 0.5603 (t0) REVERT: F 400 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: G 12 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6562 (mtp180) REVERT: G 17 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.6472 (tmt-80) REVERT: G 75 GLU cc_start: 0.7488 (tp30) cc_final: 0.6953 (tp30) REVERT: G 79 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7747 (ttpt) REVERT: G 224 LYS cc_start: 0.6264 (ttpp) cc_final: 0.5850 (pttp) REVERT: G 236 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5989 (mt) REVERT: G 306 MET cc_start: 0.4179 (mmp) cc_final: 0.3736 (mmp) REVERT: G 400 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.7059 (t-90) REVERT: G 403 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6678 (ttp-170) REVERT: H 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6405 (tmt-80) REVERT: H 75 GLU cc_start: 0.7463 (tp30) cc_final: 0.7012 (tp30) REVERT: H 79 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7829 (ttpt) REVERT: H 213 GLU cc_start: 0.7159 (mp0) cc_final: 0.6704 (mp0) REVERT: H 224 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5911 (pttp) REVERT: H 288 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6614 (mp) REVERT: H 400 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6914 (t-90) REVERT: H 403 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6881 (mtt-85) REVERT: I 12 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6273 (mtp180) REVERT: I 17 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: I 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6986 (tp30) REVERT: I 79 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7627 (mtmm) REVERT: I 224 LYS cc_start: 0.6300 (ttpp) cc_final: 0.5986 (pttp) REVERT: I 400 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6970 (t-90) REVERT: I 403 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6648 (ttp-170) REVERT: J 17 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6469 (tmt-80) REVERT: J 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7205 (tp30) REVERT: J 165 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6806 (mtt) REVERT: J 193 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: J 224 LYS cc_start: 0.6233 (ttpp) cc_final: 0.5862 (pttp) REVERT: J 236 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5928 (mt) REVERT: J 283 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5910 (mpp80) REVERT: J 306 MET cc_start: 0.4442 (mmp) cc_final: 0.4117 (mmp) REVERT: J 400 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.7010 (t-90) REVERT: K 12 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6305 (mtp180) REVERT: K 17 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6436 (tmt-80) REVERT: K 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.7020 (tp30) REVERT: K 193 GLN cc_start: 0.7356 (pt0) cc_final: 0.7080 (pt0) REVERT: K 213 GLU cc_start: 0.7104 (mp0) cc_final: 0.6778 (mp0) REVERT: K 224 LYS cc_start: 0.6201 (ttpp) cc_final: 0.5815 (pttp) REVERT: K 400 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.7039 (t-90) REVERT: K 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6646 (ttp-110) REVERT: L 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6343 (mtp180) REVERT: L 17 ARG cc_start: 0.7293 (ttp-110) cc_final: 0.6466 (tmt-80) REVERT: L 75 GLU cc_start: 0.7505 (tp30) cc_final: 0.7063 (tp30) REVERT: L 79 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7772 (ttpt) REVERT: L 193 GLN cc_start: 0.7403 (pt0) cc_final: 0.7181 (pt0) REVERT: L 224 LYS cc_start: 0.6219 (ttpp) cc_final: 0.5850 (pttp) REVERT: L 236 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5877 (mt) REVERT: L 283 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5843 (mpp80) REVERT: L 400 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6977 (t-90) REVERT: M 12 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6280 (mtp180) REVERT: M 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: M 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6977 (tp30) REVERT: M 79 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7797 (ttpt) REVERT: M 224 LYS cc_start: 0.6384 (ttpp) cc_final: 0.6083 (pttp) REVERT: M 264 ASN cc_start: 0.5940 (OUTLIER) cc_final: 0.5631 (t0) REVERT: M 400 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7005 (t-90) REVERT: N 12 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6585 (mtp180) REVERT: N 17 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6468 (tmt-80) REVERT: N 75 GLU cc_start: 0.7484 (tp30) cc_final: 0.6949 (tp30) REVERT: N 79 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7753 (ttpt) REVERT: N 224 LYS cc_start: 0.6310 (ttpp) cc_final: 0.5891 (pttp) REVERT: N 400 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.7060 (t-90) REVERT: N 403 ARG cc_start: 0.7127 (ttm-80) cc_final: 0.6711 (ttp-170) REVERT: S 26 HIS cc_start: 0.5384 (OUTLIER) cc_final: 0.5097 (t70) REVERT: T 26 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4985 (t70) outliers start: 277 outliers final: 171 residues processed: 1073 average time/residue: 1.2884 time to fit residues: 1759.0715 Evaluate side-chains 1091 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 869 time to evaluate : 4.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 193 GLN Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 264 ASN Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 232 MET Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain W residue 26 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 664 optimal weight: 0.7980 chunk 437 optimal weight: 20.0000 chunk 704 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 chunk 489 optimal weight: 7.9990 chunk 739 optimal weight: 20.0000 chunk 680 optimal weight: 4.9990 chunk 588 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN I 365 GLN J 365 GLN K 365 GLN L 365 GLN M 365 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 56042 Z= 0.389 Angle : 0.644 12.047 75712 Z= 0.331 Chirality : 0.046 0.171 9142 Planarity : 0.004 0.034 9884 Dihedral : 4.414 41.469 7917 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 4.46 % Allowed : 26.53 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 7462 helix: 1.91 (0.08), residues: 4228 sheet: 0.31 (0.19), residues: 756 loop : -1.06 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 23 HIS 0.006 0.003 HIS H 400 PHE 0.008 0.001 PHE B 194 TYR 0.013 0.001 TYR C 505 ARG 0.006 0.001 ARG N 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 873 time to evaluate : 4.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6448 (tmt-80) REVERT: A 75 GLU cc_start: 0.7490 (tp30) cc_final: 0.7102 (tp30) REVERT: A 79 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7742 (ttpt) REVERT: A 224 LYS cc_start: 0.6285 (ttpp) cc_final: 0.5815 (pttp) REVERT: A 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6606 (ttp-110) REVERT: B 17 ARG cc_start: 0.7257 (ttp-110) cc_final: 0.6452 (tmt-80) REVERT: B 75 GLU cc_start: 0.7482 (tp30) cc_final: 0.7028 (tp30) REVERT: B 79 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7631 (mtmm) REVERT: B 224 LYS cc_start: 0.6303 (ttpp) cc_final: 0.5802 (pttp) REVERT: B 400 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6898 (t-90) REVERT: B 403 ARG cc_start: 0.7129 (ttm-80) cc_final: 0.6631 (ttp-110) REVERT: C 17 ARG cc_start: 0.7311 (ttp-110) cc_final: 0.6498 (tmt-80) REVERT: C 75 GLU cc_start: 0.7474 (tp30) cc_final: 0.7094 (tp30) REVERT: C 165 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6859 (mtt) REVERT: C 193 GLN cc_start: 0.7437 (pt0) cc_final: 0.7147 (pt0) REVERT: C 224 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5746 (pttp) REVERT: C 236 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5953 (mt) REVERT: C 283 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.5866 (mpp80) REVERT: C 306 MET cc_start: 0.4375 (mmp) cc_final: 0.3907 (mmp) REVERT: C 400 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6907 (t-90) REVERT: D 12 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6274 (mtp180) REVERT: D 17 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6467 (tmt-80) REVERT: D 75 GLU cc_start: 0.7510 (tp30) cc_final: 0.7064 (tp30) REVERT: D 213 GLU cc_start: 0.7057 (mp0) cc_final: 0.6528 (mp0) REVERT: D 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5767 (pttp) REVERT: D 400 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6958 (t-90) REVERT: D 403 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6628 (ttp-110) REVERT: E 12 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.6418 (mtp180) REVERT: E 17 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6475 (tmt-80) REVERT: E 75 GLU cc_start: 0.7538 (tp30) cc_final: 0.7076 (tp30) REVERT: E 224 LYS cc_start: 0.6140 (ttpp) cc_final: 0.5709 (pttp) REVERT: E 236 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5932 (mt) REVERT: E 283 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5937 (mpp80) REVERT: E 400 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6874 (t-90) REVERT: F 12 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6284 (mtp180) REVERT: F 17 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6445 (tmt-80) REVERT: F 75 GLU cc_start: 0.7521 (tp30) cc_final: 0.7086 (tp30) REVERT: F 193 GLN cc_start: 0.7495 (pt0) cc_final: 0.7222 (pt0) REVERT: F 224 LYS cc_start: 0.6362 (ttpp) cc_final: 0.5999 (pttp) REVERT: F 264 ASN cc_start: 0.5869 (OUTLIER) cc_final: 0.5555 (t0) REVERT: F 400 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6907 (t-90) REVERT: G 12 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.6480 (mtp180) REVERT: G 17 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6457 (tmt-80) REVERT: G 75 GLU cc_start: 0.7509 (tp30) cc_final: 0.7012 (tp30) REVERT: G 224 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5755 (pttp) REVERT: G 236 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5964 (mt) REVERT: G 400 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: G 403 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6669 (ttp-170) REVERT: H 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6447 (tmt-80) REVERT: H 75 GLU cc_start: 0.7491 (tp30) cc_final: 0.7101 (tp30) REVERT: H 79 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7739 (ttpt) REVERT: H 224 LYS cc_start: 0.6283 (ttpp) cc_final: 0.5813 (pttp) REVERT: H 403 ARG cc_start: 0.7106 (ttm-80) cc_final: 0.6607 (ttp-110) REVERT: I 12 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6284 (mtp180) REVERT: I 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6455 (tmt-80) REVERT: I 75 GLU cc_start: 0.7484 (tp30) cc_final: 0.7034 (tp30) REVERT: I 79 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7700 (mtmm) REVERT: I 224 LYS cc_start: 0.6302 (ttpp) cc_final: 0.5802 (pttp) REVERT: I 400 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6893 (t-90) REVERT: I 403 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6636 (ttm-80) REVERT: J 17 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.6497 (tmt-80) REVERT: J 75 GLU cc_start: 0.7475 (tp30) cc_final: 0.7095 (tp30) REVERT: J 165 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: J 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5758 (pttp) REVERT: J 236 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5950 (mt) REVERT: J 283 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.5889 (mpp80) REVERT: J 306 MET cc_start: 0.4373 (mmp) cc_final: 0.4012 (mmp) REVERT: J 400 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6915 (t-90) REVERT: K 12 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6275 (mtp180) REVERT: K 17 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6462 (tmt-80) REVERT: K 75 GLU cc_start: 0.7511 (tp30) cc_final: 0.7065 (tp30) REVERT: K 213 GLU cc_start: 0.7073 (mp0) cc_final: 0.6566 (mp0) REVERT: K 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5762 (pttp) REVERT: K 400 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: K 403 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6627 (ttp-110) REVERT: L 12 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6412 (mtp180) REVERT: L 17 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6476 (tmt-80) REVERT: L 75 GLU cc_start: 0.7535 (tp30) cc_final: 0.7072 (tp30) REVERT: L 224 LYS cc_start: 0.6159 (ttpp) cc_final: 0.5697 (pttp) REVERT: L 236 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5983 (mt) REVERT: L 283 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5775 (mpp80) REVERT: L 400 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6883 (t-90) REVERT: M 12 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6281 (mtp180) REVERT: M 17 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.6444 (tmt-80) REVERT: M 75 GLU cc_start: 0.7521 (tp30) cc_final: 0.7089 (tp30) REVERT: M 193 GLN cc_start: 0.7491 (pt0) cc_final: 0.7218 (pt0) REVERT: M 224 LYS cc_start: 0.6354 (ttpp) cc_final: 0.5999 (pttp) REVERT: M 264 ASN cc_start: 0.5818 (OUTLIER) cc_final: 0.5544 (t0) REVERT: M 400 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: N 12 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6501 (mtp180) REVERT: N 17 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6454 (tmt-80) REVERT: N 75 GLU cc_start: 0.7509 (tp30) cc_final: 0.7014 (tp30) REVERT: N 224 LYS cc_start: 0.6253 (ttpp) cc_final: 0.5818 (pttp) REVERT: N 400 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: N 403 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6675 (ttp-170) REVERT: S 26 HIS cc_start: 0.5415 (OUTLIER) cc_final: 0.5109 (t70) REVERT: T 26 HIS cc_start: 0.5352 (OUTLIER) cc_final: 0.5058 (t70) outliers start: 260 outliers final: 173 residues processed: 1064 average time/residue: 1.3148 time to fit residues: 1773.6523 Evaluate side-chains 1068 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 855 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 230 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 402 THR Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 402 THR Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 402 THR Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 360 optimal weight: 4.9990 chunk 467 optimal weight: 2.9990 chunk 627 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 542 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 589 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 605 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN E 365 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 GLN G 318 GLN G 365 GLN H 365 GLN I 365 GLN J 365 GLN K 365 GLN ** M 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN N 365 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124727 restraints weight = 54924.501| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.72 r_work: 0.3265 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 56042 Z= 0.287 Angle : 0.590 10.794 75712 Z= 0.304 Chirality : 0.043 0.166 9142 Planarity : 0.004 0.035 9884 Dihedral : 4.314 45.698 7917 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.27 % Favored : 96.54 % Rotamer: Outliers : 4.22 % Allowed : 26.84 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 7462 helix: 1.98 (0.08), residues: 4228 sheet: 0.28 (0.19), residues: 756 loop : -1.08 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 23 HIS 0.004 0.002 HIS A 400 PHE 0.008 0.001 PHE G 194 TYR 0.011 0.001 TYR F 505 ARG 0.004 0.001 ARG E 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27650.84 seconds wall clock time: 474 minutes 50.84 seconds (28490.84 seconds total)