Starting phenix.real_space_refine on Tue Mar 19 01:00:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/03_2024/7sn7_25213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/03_2024/7sn7_25213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/03_2024/7sn7_25213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/03_2024/7sn7_25213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/03_2024/7sn7_25213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/03_2024/7sn7_25213.pdb" } resolution = 4.2 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= 0.004 sd= 0.070 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 138 5.16 5 C 54556 2.51 5 N 15778 2.21 5 O 20010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 84": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E ASP 465": "OD1" <-> "OD2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 514": "OE1" <-> "OE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "H ASP 44": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "I ASP 220": "OD1" <-> "OD2" Residue "I TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 455": "OE1" <-> "OE2" Residue "I ASP 486": "OD1" <-> "OD2" Residue "I GLU 501": "OE1" <-> "OE2" Residue "J ASP 44": "OD1" <-> "OD2" Residue "J PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 166": "OD1" <-> "OD2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 413": "OD1" <-> "OD2" Residue "J GLU 430": "OE1" <-> "OE2" Residue "J ASP 486": "OD1" <-> "OD2" Residue "J GLU 514": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "K PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "L ASP 124": "OD1" <-> "OD2" Residue "L TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 501": "OE1" <-> "OE2" Residue "M TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N ASP 264": "OD1" <-> "OD2" Residue "N PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 472": "OD1" <-> "OD2" Residue "O GLU 30": "OE1" <-> "OE2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "O GLU 180": "OE1" <-> "OE2" Residue "O PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 455": "OE1" <-> "OE2" Residue "O GLU 514": "OE1" <-> "OE2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "a GLU 79": "OE1" <-> "OE2" Residue "a ASP 110": "OD1" <-> "OD2" Residue "a PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 486": "OD1" <-> "OD2" Residue "b GLU 30": "OE1" <-> "OE2" Residue "b ASP 44": "OD1" <-> "OD2" Residue "b ASP 70": "OD1" <-> "OD2" Residue "b ASP 159": "OD1" <-> "OD2" Residue "b TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 455": "OE1" <-> "OE2" Residue "b TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 44": "OD1" <-> "OD2" Residue "d ASP 141": "OD1" <-> "OD2" Residue "d TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 413": "OD1" <-> "OD2" Residue "d TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 486": "OD1" <-> "OD2" Residue "d GLU 501": "OE1" <-> "OE2" Residue "e GLU 79": "OE1" <-> "OE2" Residue "e GLU 84": "OE1" <-> "OE2" Residue "e ASP 114": "OD1" <-> "OD2" Residue "e PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 431": "OD1" <-> "OD2" Residue "f GLU 84": "OE1" <-> "OE2" Residue "f ASP 114": "OD1" <-> "OD2" Residue "f TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 293": "OD1" <-> "OD2" Residue "f ASP 381": "OD1" <-> "OD2" Residue "f TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 501": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g ASP 141": "OD1" <-> "OD2" Residue "g ASP 166": "OD1" <-> "OD2" Residue "g TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 486": "OD1" <-> "OD2" Residue "g GLU 514": "OE1" <-> "OE2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h ASP 141": "OD1" <-> "OD2" Residue "h GLU 455": "OE1" <-> "OE2" Residue "h PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90482 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "B" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "C" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "D" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "E" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "F" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "G" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "H" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "I" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "J" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "K" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "L" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "M" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "N" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "O" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "a" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "b" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "c" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "d" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "e" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "f" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "g" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "h" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Time building chain proxies: 33.56, per 1000 atoms: 0.37 Number of scatterers: 90482 At special positions: 0 Unit cell: (251.64, 231.12, 341.28, 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 138 16.00 O 20010 8.00 N 15778 7.00 C 54556 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: 29.51 Conformation dependent library (CDL) restraints added in 12.8 seconds 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23092 Finding SS restraints... Secondary structure from input PDB file: 273 helices and 196 sheets defined 44.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 3.713A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 100 Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.538A pdb=" N THR A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.615A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.648A pdb=" N THR A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 459 through 507 removed outlier: 3.530A pdb=" N ILE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 538 removed outlier: 3.657A pdb=" N SER A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.509A pdb=" N GLN A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.805A pdb=" N THR B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 100 Processing helix chain 'B' and resid 105 through 130 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.796A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.594A pdb=" N THR B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 459 through 507 removed outlier: 3.925A pdb=" N ILE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.889A pdb=" N SER B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.001A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 100 Processing helix chain 'C' and resid 105 through 130 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 217 through 228 removed outlier: 3.696A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 333 through 345 removed outlier: 4.113A pdb=" N THR C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 459 through 505 removed outlier: 3.749A pdb=" N ALA C 463 " --> pdb=" O ASP C 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 464 " --> pdb=" O PRO C 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 537 removed outlier: 3.668A pdb=" N SER C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 547 removed outlier: 4.255A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 3.697A pdb=" N THR D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 23 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 100 Processing helix chain 'D' and resid 105 through 130 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 217 through 228 removed outlier: 3.629A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.629A pdb=" N THR D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 459 through 507 removed outlier: 3.544A pdb=" N ARG D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 537 removed outlier: 3.747A pdb=" N SER D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 Processing helix chain 'E' and resid 10 through 35 removed outlier: 3.772A pdb=" N THR E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 100 Processing helix chain 'E' and resid 105 through 130 removed outlier: 3.570A pdb=" N THR E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 217 through 228 removed outlier: 3.769A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'E' and resid 333 through 345 removed outlier: 3.935A pdb=" N THR E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 459 through 505 removed outlier: 4.121A pdb=" N ASP E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 537 removed outlier: 3.549A pdb=" N GLU E 514 " --> pdb=" O ASP E 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 547 Processing helix chain 'F' and resid 10 through 35 removed outlier: 3.691A pdb=" N THR F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 100 Processing helix chain 'F' and resid 105 through 130 Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 217 through 228 removed outlier: 3.780A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 333 through 345 removed outlier: 3.651A pdb=" N THR F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 459 through 507 removed outlier: 3.640A pdb=" N ILE F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 537 removed outlier: 3.840A pdb=" N SER F 516 " --> pdb=" O ALA F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 547 Processing helix chain 'G' and resid 10 through 35 removed outlier: 3.870A pdb=" N THR G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 100 Processing helix chain 'G' and resid 105 through 130 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 217 through 228 removed outlier: 3.571A pdb=" N ALA G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 276 Processing helix chain 'G' and resid 333 through 345 removed outlier: 4.172A pdb=" N THR G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 379 through 381 No H-bonds generated for 'chain 'G' and resid 379 through 381' Processing helix chain 'G' and resid 459 through 505 removed outlier: 3.603A pdb=" N ALA G 463 " --> pdb=" O ASP G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 537 removed outlier: 3.602A pdb=" N GLU G 514 " --> pdb=" O ASP G 510 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 547 Processing helix chain 'H' and resid 10 through 35 removed outlier: 3.595A pdb=" N SER H 23 " --> pdb=" O ASN H 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 100 Processing helix chain 'H' and resid 105 through 130 removed outlier: 3.579A pdb=" N THR H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'H' and resid 217 through 228 removed outlier: 3.536A pdb=" N ALA H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 276 Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.546A pdb=" N THR H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 459 through 507 removed outlier: 3.691A pdb=" N ILE H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 537 removed outlier: 4.031A pdb=" N GLU H 514 " --> pdb=" O ASP H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 546 Processing helix chain 'I' and resid 10 through 35 removed outlier: 3.707A pdb=" N THR I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 100 Processing helix chain 'I' and resid 105 through 130 Processing helix chain 'I' and resid 164 through 169 Processing helix chain 'I' and resid 187 through 191 Processing helix chain 'I' and resid 217 through 228 removed outlier: 3.743A pdb=" N ALA I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 276 removed outlier: 3.563A pdb=" N ASN I 276 " --> pdb=" O ALA I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 345 removed outlier: 3.572A pdb=" N THR I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 378 Processing helix chain 'I' and resid 459 through 505 removed outlier: 3.776A pdb=" N ALA I 463 " --> pdb=" O ASP I 459 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 464 " --> pdb=" O PRO I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 537 removed outlier: 3.617A pdb=" N SER I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 547 Processing helix chain 'J' and resid 10 through 35 removed outlier: 3.915A pdb=" N THR J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER J 23 " --> pdb=" O ASN J 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 100 Processing helix chain 'J' and resid 105 through 130 Processing helix chain 'J' and resid 164 through 169 Processing helix chain 'J' and resid 187 through 191 Processing helix chain 'J' and resid 217 through 228 removed outlier: 3.661A pdb=" N ALA J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 276 Processing helix chain 'J' and resid 333 through 345 removed outlier: 3.680A pdb=" N THR J 339 " --> pdb=" O ALA J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 378 Processing helix chain 'J' and resid 459 through 505 Processing helix chain 'J' and resid 510 through 537 removed outlier: 3.829A pdb=" N SER J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 547 Processing helix chain 'K' and resid 10 through 35 removed outlier: 3.762A pdb=" N THR K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 100 Processing helix chain 'K' and resid 105 through 130 removed outlier: 3.655A pdb=" N THR K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 187 through 191 Processing helix chain 'K' and resid 217 through 228 removed outlier: 3.519A pdb=" N ALA K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 276 Processing helix chain 'K' and resid 333 through 345 removed outlier: 3.617A pdb=" N THR K 339 " --> pdb=" O ALA K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 379 Processing helix chain 'K' and resid 459 through 507 Processing helix chain 'K' and resid 510 through 538 removed outlier: 3.541A pdb=" N GLU K 514 " --> pdb=" O ASP K 510 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER K 516 " --> pdb=" O ALA K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 547 removed outlier: 3.554A pdb=" N GLN K 547 " --> pdb=" O LEU K 543 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 35 removed outlier: 3.756A pdb=" N THR L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 100 Processing helix chain 'L' and resid 105 through 130 removed outlier: 3.525A pdb=" N THR L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 169 Processing helix chain 'L' and resid 187 through 191 Processing helix chain 'L' and resid 217 through 228 Processing helix chain 'L' and resid 270 through 276 Processing helix chain 'L' and resid 333 through 345 removed outlier: 3.546A pdb=" N THR L 339 " --> pdb=" O ALA L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 378 Processing helix chain 'L' and resid 459 through 505 removed outlier: 3.580A pdb=" N ALA L 463 " --> pdb=" O ASP L 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG L 505 " --> pdb=" O GLU L 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 537 removed outlier: 3.727A pdb=" N SER L 516 " --> pdb=" O ALA L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 547 Processing helix chain 'M' and resid 10 through 35 removed outlier: 3.813A pdb=" N THR M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER M 23 " --> pdb=" O ASN M 19 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 100 Processing helix chain 'M' and resid 105 through 130 Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.668A pdb=" N ALA M 139 " --> pdb=" O ASN M 136 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS M 140 " --> pdb=" O VAL M 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 136 through 140' Processing helix chain 'M' and resid 164 through 169 Processing helix chain 'M' and resid 217 through 228 removed outlier: 3.644A pdb=" N ALA M 228 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 276 Processing helix chain 'M' and resid 333 through 345 removed outlier: 3.835A pdb=" N THR M 339 " --> pdb=" O ALA M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 379 Processing helix chain 'M' and resid 459 through 507 Processing helix chain 'M' and resid 510 through 537 removed outlier: 3.558A pdb=" N GLU M 514 " --> pdb=" O ASP M 510 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER M 516 " --> pdb=" O ALA M 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 547 removed outlier: 3.728A pdb=" N GLN M 547 " --> pdb=" O LEU M 543 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 35 removed outlier: 3.661A pdb=" N SER N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 100 Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.572A pdb=" N THR N 130 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 169 Processing helix chain 'N' and resid 187 through 191 Processing helix chain 'N' and resid 217 through 228 removed outlier: 3.663A pdb=" N ALA N 228 " --> pdb=" O ALA N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 276 Processing helix chain 'N' and resid 333 through 345 Processing helix chain 'N' and resid 370 through 378 Processing helix chain 'N' and resid 459 through 507 removed outlier: 3.516A pdb=" N ALA N 463 " --> pdb=" O ASP N 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE N 506 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 537 removed outlier: 3.769A pdb=" N SER N 516 " --> pdb=" O ALA N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 547 Processing helix chain 'O' and resid 10 through 35 removed outlier: 3.891A pdb=" N THR O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 Processing helix chain 'O' and resid 105 through 130 removed outlier: 3.552A pdb=" N THR O 130 " --> pdb=" O VAL O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 191 removed outlier: 3.823A pdb=" N MET O 191 " --> pdb=" O LEU O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 217 through 228 removed outlier: 3.781A pdb=" N ALA O 228 " --> pdb=" O ALA O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 333 through 345 removed outlier: 3.549A pdb=" N THR O 339 " --> pdb=" O ALA O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 370 through 379 Processing helix chain 'O' and resid 459 through 507 removed outlier: 3.560A pdb=" N ILE O 506 " --> pdb=" O ALA O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 510 through 537 removed outlier: 3.558A pdb=" N GLU O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER O 516 " --> pdb=" O ALA O 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 547 Processing helix chain 'a' and resid 10 through 35 removed outlier: 3.680A pdb=" N SER a 23 " --> pdb=" O ASN a 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA a 24 " --> pdb=" O LYS a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 100 Processing helix chain 'a' and resid 105 through 130 Processing helix chain 'a' and resid 164 through 169 Processing helix chain 'a' and resid 217 through 228 removed outlier: 3.845A pdb=" N ALA a 228 " --> pdb=" O ALA a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 270 through 276 Processing helix chain 'a' and resid 333 through 345 removed outlier: 3.627A pdb=" N THR a 339 " --> pdb=" O ALA a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 370 through 378 Processing helix chain 'a' and resid 459 through 505 Processing helix chain 'a' and resid 510 through 537 removed outlier: 3.799A pdb=" N GLU a 514 " --> pdb=" O ASP a 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER a 516 " --> pdb=" O ALA a 512 " (cutoff:3.500A) Processing helix chain 'a' and resid 540 through 547 Processing helix chain 'b' and resid 10 through 35 removed outlier: 3.997A pdb=" N THR b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER b 23 " --> pdb=" O ASN b 19 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 24 " --> pdb=" O LYS b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 100 Processing helix chain 'b' and resid 105 through 129 Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'b' and resid 217 through 228 removed outlier: 3.719A pdb=" N ALA b 228 " --> pdb=" O ALA b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 270 through 276 removed outlier: 3.573A pdb=" N ASN b 276 " --> pdb=" O ALA b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.738A pdb=" N THR b 339 " --> pdb=" O ALA b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 370 through 378 Processing helix chain 'b' and resid 459 through 505 removed outlier: 3.826A pdb=" N ALA b 463 " --> pdb=" O ASP b 459 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU b 464 " --> pdb=" O PRO b 460 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG b 505 " --> pdb=" O GLU b 501 " (cutoff:3.500A) Processing helix chain 'b' and resid 510 through 537 removed outlier: 3.635A pdb=" N SER b 516 " --> pdb=" O ALA b 512 " (cutoff:3.500A) Processing helix chain 'b' and resid 540 through 547 Processing helix chain 'c' and resid 10 through 35 removed outlier: 3.507A pdb=" N SER c 23 " --> pdb=" O ASN c 19 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA c 24 " --> pdb=" O LYS c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 100 Processing helix chain 'c' and resid 105 through 130 Processing helix chain 'c' and resid 164 through 169 Processing helix chain 'c' and resid 217 through 228 removed outlier: 3.650A pdb=" N ALA c 228 " --> pdb=" O ALA c 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 270 through 276 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.625A pdb=" N THR c 339 " --> pdb=" O ALA c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 370 through 378 Processing helix chain 'c' and resid 459 through 507 removed outlier: 3.622A pdb=" N ALA c 463 " --> pdb=" O ASP c 459 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE c 506 " --> pdb=" O ALA c 502 " (cutoff:3.500A) Processing helix chain 'c' and resid 510 through 537 removed outlier: 3.826A pdb=" N SER c 516 " --> pdb=" O ALA c 512 " (cutoff:3.500A) Processing helix chain 'c' and resid 540 through 547 Processing helix chain 'd' and resid 10 through 35 removed outlier: 3.582A pdb=" N THR d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER d 23 " --> pdb=" O ASN d 19 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA d 24 " --> pdb=" O LYS d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 100 Processing helix chain 'd' and resid 105 through 130 Processing helix chain 'd' and resid 164 through 169 Processing helix chain 'd' and resid 187 through 191 Processing helix chain 'd' and resid 217 through 228 removed outlier: 3.516A pdb=" N ALA d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 270 through 276 Processing helix chain 'd' and resid 333 through 345 removed outlier: 3.529A pdb=" N THR d 339 " --> pdb=" O ALA d 335 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 378 Processing helix chain 'd' and resid 459 through 507 removed outlier: 3.731A pdb=" N ILE d 506 " --> pdb=" O ALA d 502 " (cutoff:3.500A) Processing helix chain 'd' and resid 510 through 537 removed outlier: 3.649A pdb=" N SER d 516 " --> pdb=" O ALA d 512 " (cutoff:3.500A) Processing helix chain 'd' and resid 539 through 547 removed outlier: 4.321A pdb=" N LEU d 543 " --> pdb=" O PRO d 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 35 removed outlier: 3.513A pdb=" N THR e 14 " --> pdb=" O LEU e 10 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER e 23 " --> pdb=" O ASN e 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA e 24 " --> pdb=" O LYS e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 100 Processing helix chain 'e' and resid 105 through 130 removed outlier: 3.612A pdb=" N THR e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 169 Processing helix chain 'e' and resid 187 through 191 removed outlier: 3.508A pdb=" N MET e 191 " --> pdb=" O LEU e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 228 removed outlier: 3.892A pdb=" N ALA e 228 " --> pdb=" O ALA e 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 270 through 276 Processing helix chain 'e' and resid 333 through 345 removed outlier: 3.557A pdb=" N THR e 339 " --> pdb=" O ALA e 335 " (cutoff:3.500A) Processing helix chain 'e' and resid 370 through 378 Processing helix chain 'e' and resid 379 through 381 No H-bonds generated for 'chain 'e' and resid 379 through 381' Processing helix chain 'e' and resid 459 through 505 Processing helix chain 'e' and resid 510 through 538 removed outlier: 3.827A pdb=" N GLU e 514 " --> pdb=" O ASP e 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER e 516 " --> pdb=" O ALA e 512 " (cutoff:3.500A) Processing helix chain 'e' and resid 540 through 547 removed outlier: 3.709A pdb=" N GLN e 547 " --> pdb=" O LEU e 543 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 35 removed outlier: 3.891A pdb=" N THR f 14 " --> pdb=" O LEU f 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER f 23 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 100 Processing helix chain 'f' and resid 105 through 130 Processing helix chain 'f' and resid 164 through 169 Processing helix chain 'f' and resid 187 through 191 Processing helix chain 'f' and resid 217 through 228 removed outlier: 3.761A pdb=" N ALA f 228 " --> pdb=" O ALA f 224 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 276 Processing helix chain 'f' and resid 333 through 345 removed outlier: 3.708A pdb=" N THR f 339 " --> pdb=" O ALA f 335 " (cutoff:3.500A) Processing helix chain 'f' and resid 370 through 378 Processing helix chain 'f' and resid 459 through 507 removed outlier: 3.592A pdb=" N ALA f 463 " --> pdb=" O ASP f 459 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG f 505 " --> pdb=" O GLU f 501 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE f 506 " --> pdb=" O ALA f 502 " (cutoff:3.500A) Processing helix chain 'f' and resid 510 through 537 removed outlier: 3.616A pdb=" N GLU f 514 " --> pdb=" O ASP f 510 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER f 516 " --> pdb=" O ALA f 512 " (cutoff:3.500A) Processing helix chain 'f' and resid 540 through 547 removed outlier: 3.610A pdb=" N GLN f 547 " --> pdb=" O LEU f 543 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 35 removed outlier: 3.743A pdb=" N THR g 14 " --> pdb=" O LEU g 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER g 23 " --> pdb=" O ASN g 19 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA g 24 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 100 Processing helix chain 'g' and resid 105 through 130 Processing helix chain 'g' and resid 164 through 169 Processing helix chain 'g' and resid 187 through 191 Processing helix chain 'g' and resid 217 through 228 removed outlier: 3.686A pdb=" N ALA g 228 " --> pdb=" O ALA g 224 " (cutoff:3.500A) Processing helix chain 'g' and resid 270 through 276 Processing helix chain 'g' and resid 333 through 345 removed outlier: 3.534A pdb=" N THR g 339 " --> pdb=" O ALA g 335 " (cutoff:3.500A) Processing helix chain 'g' and resid 370 through 378 Processing helix chain 'g' and resid 459 through 507 removed outlier: 3.507A pdb=" N LEU g 464 " --> pdb=" O PRO g 460 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE g 506 " --> pdb=" O ALA g 502 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 537 removed outlier: 3.513A pdb=" N SER g 516 " --> pdb=" O ALA g 512 " (cutoff:3.500A) Processing helix chain 'g' and resid 539 through 547 removed outlier: 4.102A pdb=" N LEU g 543 " --> pdb=" O PRO g 539 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 35 removed outlier: 3.979A pdb=" N THR h 14 " --> pdb=" O LEU h 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER h 23 " --> pdb=" O ASN h 19 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA h 24 " --> pdb=" O LYS h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 100 Processing helix chain 'h' and resid 105 through 130 Processing helix chain 'h' and resid 164 through 169 Processing helix chain 'h' and resid 217 through 228 Processing helix chain 'h' and resid 270 through 276 removed outlier: 3.617A pdb=" N PHE h 274 " --> pdb=" O ASN h 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 333 through 345 removed outlier: 3.787A pdb=" N THR h 339 " --> pdb=" O ALA h 335 " (cutoff:3.500A) Processing helix chain 'h' and resid 370 through 378 Processing helix chain 'h' and resid 459 through 505 Processing helix chain 'h' and resid 510 through 537 removed outlier: 3.679A pdb=" N SER h 516 " --> pdb=" O ALA h 512 " (cutoff:3.500A) Processing helix chain 'h' and resid 539 through 547 removed outlier: 4.117A pdb=" N LEU h 543 " --> pdb=" O PRO h 539 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN h 547 " --> pdb=" O LEU h 543 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 288 Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA8, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 288 Processing sheet with id=AB3, first strand: chain 'B' and resid 314 through 315 removed outlier: 3.562A pdb=" N ASN B 324 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 387 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 147 Processing sheet with id=AB9, first strand: chain 'C' and resid 179 through 182 removed outlier: 3.975A pdb=" N GLY C 179 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'C' and resid 260 through 263 removed outlier: 5.765A pdb=" N ALA C 261 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER C 366 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 283 through 288 Processing sheet with id=AC4, first strand: chain 'C' and resid 314 through 315 removed outlier: 3.594A pdb=" N ASN C 324 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AC7, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AC8, first strand: chain 'D' and resid 143 through 147 Processing sheet with id=AC9, first strand: chain 'D' and resid 181 through 182 removed outlier: 3.710A pdb=" N THR D 181 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 452 " --> pdb=" O THR D 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 194 through 196 Processing sheet with id=AD2, first strand: chain 'D' and resid 283 through 288 Processing sheet with id=AD3, first strand: chain 'D' and resid 314 through 315 removed outlier: 3.706A pdb=" N ASN D 324 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AD5, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AD6, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD7, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AD8, first strand: chain 'E' and resid 194 through 196 Processing sheet with id=AD9, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AE1, first strand: chain 'E' and resid 283 through 288 Processing sheet with id=AE2, first strand: chain 'E' and resid 314 through 315 Processing sheet with id=AE3, first strand: chain 'E' and resid 355 through 357 Processing sheet with id=AE4, first strand: chain 'E' and resid 386 through 387 Processing sheet with id=AE5, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AE6, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AE7, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AE8, first strand: chain 'F' and resid 194 through 196 Processing sheet with id=AE9, first strand: chain 'F' and resid 260 through 261 Processing sheet with id=AF1, first strand: chain 'F' and resid 283 through 288 Processing sheet with id=AF2, first strand: chain 'F' and resid 314 through 315 removed outlier: 3.606A pdb=" N ASN F 324 " --> pdb=" O TYR F 314 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AF4, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AF5, first strand: chain 'F' and resid 405 through 406 Processing sheet with id=AF6, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AF7, first strand: chain 'G' and resid 143 through 147 Processing sheet with id=AF8, first strand: chain 'G' and resid 179 through 182 removed outlier: 4.106A pdb=" N GLY G 179 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 194 through 196 Processing sheet with id=AG1, first strand: chain 'G' and resid 260 through 261 Processing sheet with id=AG2, first strand: chain 'G' and resid 283 through 288 Processing sheet with id=AG3, first strand: chain 'G' and resid 314 through 315 Processing sheet with id=AG4, first strand: chain 'G' and resid 355 through 357 Processing sheet with id=AG5, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AG6, first strand: chain 'G' and resid 405 through 406 Processing sheet with id=AG7, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AG8, first strand: chain 'H' and resid 143 through 147 Processing sheet with id=AG9, first strand: chain 'H' and resid 194 through 196 Processing sheet with id=AH1, first strand: chain 'H' and resid 260 through 261 Processing sheet with id=AH2, first strand: chain 'H' and resid 283 through 288 Processing sheet with id=AH3, first strand: chain 'H' and resid 314 through 315 removed outlier: 3.664A pdb=" N ASN H 324 " --> pdb=" O TYR H 314 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 355 through 357 Processing sheet with id=AH5, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AH6, first strand: chain 'H' and resid 405 through 406 Processing sheet with id=AH7, first strand: chain 'I' and resid 143 through 147 Processing sheet with id=AH8, first strand: chain 'I' and resid 179 through 182 removed outlier: 4.149A pdb=" N GLY I 179 " --> pdb=" O ALA I 454 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 194 through 196 Processing sheet with id=AI1, first strand: chain 'I' and resid 260 through 261 Processing sheet with id=AI2, first strand: chain 'I' and resid 283 through 288 Processing sheet with id=AI3, first strand: chain 'I' and resid 314 through 315 Processing sheet with id=AI4, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AI5, first strand: chain 'I' and resid 382 through 383 Processing sheet with id=AI6, first strand: chain 'I' and resid 386 through 387 Processing sheet with id=AI7, first strand: chain 'I' and resid 405 through 406 Processing sheet with id=AI8, first strand: chain 'J' and resid 143 through 147 Processing sheet with id=AI9, first strand: chain 'J' and resid 194 through 196 Processing sheet with id=AJ1, first strand: chain 'J' and resid 260 through 261 Processing sheet with id=AJ2, first strand: chain 'J' and resid 283 through 288 Processing sheet with id=AJ3, first strand: chain 'J' and resid 314 through 315 removed outlier: 3.732A pdb=" N ASN J 324 " --> pdb=" O TYR J 314 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 355 through 357 Processing sheet with id=AJ5, first strand: chain 'J' and resid 386 through 387 Processing sheet with id=AJ6, first strand: chain 'J' and resid 405 through 406 Processing sheet with id=AJ7, first strand: chain 'K' and resid 143 through 147 Processing sheet with id=AJ8, first strand: chain 'K' and resid 194 through 196 Processing sheet with id=AJ9, first strand: chain 'K' and resid 283 through 288 Processing sheet with id=AK1, first strand: chain 'K' and resid 314 through 315 removed outlier: 4.041A pdb=" N ASN K 324 " --> pdb=" O TYR K 314 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'K' and resid 355 through 357 Processing sheet with id=AK3, first strand: chain 'K' and resid 386 through 387 Processing sheet with id=AK4, first strand: chain 'K' and resid 405 through 406 Processing sheet with id=AK5, first strand: chain 'L' and resid 131 through 132 Processing sheet with id=AK6, first strand: chain 'L' and resid 143 through 147 Processing sheet with id=AK7, first strand: chain 'L' and resid 181 through 182 removed outlier: 3.874A pdb=" N THR L 181 " --> pdb=" O SER L 452 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'L' and resid 194 through 196 Processing sheet with id=AK9, first strand: chain 'L' and resid 260 through 265 removed outlier: 3.529A pdb=" N MET L 367 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER L 263 " --> pdb=" O ALA L 365 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA L 365 " --> pdb=" O SER L 263 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP L 265 " --> pdb=" O ASP L 363 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP L 363 " --> pdb=" O ASP L 265 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'L' and resid 283 through 288 Processing sheet with id=AL2, first strand: chain 'L' and resid 314 through 315 Processing sheet with id=AL3, first strand: chain 'L' and resid 386 through 387 Processing sheet with id=AL4, first strand: chain 'L' and resid 405 through 406 Processing sheet with id=AL5, first strand: chain 'M' and resid 143 through 147 Processing sheet with id=AL6, first strand: chain 'M' and resid 194 through 196 Processing sheet with id=AL7, first strand: chain 'M' and resid 263 through 265 removed outlier: 3.579A pdb=" N SER M 263 " --> pdb=" O GLY M 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP M 265 " --> pdb=" O PHE M 362 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE M 362 " --> pdb=" O ASP M 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA M 361 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP M 358 " --> pdb=" O ALA M 361 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'M' and resid 283 through 288 Processing sheet with id=AL9, first strand: chain 'M' and resid 314 through 315 removed outlier: 3.940A pdb=" N ASN M 324 " --> pdb=" O TYR M 314 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'M' and resid 386 through 387 Processing sheet with id=AM2, first strand: chain 'M' and resid 405 through 406 Processing sheet with id=AM3, first strand: chain 'N' and resid 143 through 147 Processing sheet with id=AM4, first strand: chain 'N' and resid 181 through 182 removed outlier: 3.580A pdb=" N THR N 181 " --> pdb=" O SER N 452 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 194 through 196 Processing sheet with id=AM6, first strand: chain 'N' and resid 283 through 288 Processing sheet with id=AM7, first strand: chain 'N' and resid 314 through 315 removed outlier: 4.035A pdb=" N TYR N 314 " --> pdb=" O ASN N 324 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN N 324 " --> pdb=" O TYR N 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM7 Processing sheet with id=AM8, first strand: chain 'N' and resid 355 through 357 Processing sheet with id=AM9, first strand: chain 'N' and resid 386 through 387 Processing sheet with id=AN1, first strand: chain 'N' and resid 405 through 406 removed outlier: 3.592A pdb=" N TYR N 405 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER N 412 " --> pdb=" O TYR N 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN1 Processing sheet with id=AN2, first strand: chain 'O' and resid 143 through 147 Processing sheet with id=AN3, first strand: chain 'O' and resid 194 through 196 removed outlier: 3.512A pdb=" N THR O 207 " --> pdb=" O ALA O 420 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'O' and resid 260 through 261 removed outlier: 3.571A pdb=" N MET O 367 " --> pdb=" O ALA O 261 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'O' and resid 283 through 288 Processing sheet with id=AN6, first strand: chain 'O' and resid 314 through 315 Processing sheet with id=AN7, first strand: chain 'O' and resid 355 through 357 Processing sheet with id=AN8, first strand: chain 'O' and resid 386 through 387 Processing sheet with id=AN9, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AO1, first strand: chain 'a' and resid 143 through 147 Processing sheet with id=AO2, first strand: chain 'a' and resid 194 through 196 Processing sheet with id=AO3, first strand: chain 'a' and resid 260 through 261 removed outlier: 3.718A pdb=" N MET a 367 " --> pdb=" O ALA a 261 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'a' and resid 283 through 288 Processing sheet with id=AO5, first strand: chain 'a' and resid 314 through 315 Processing sheet with id=AO6, first strand: chain 'a' and resid 355 through 357 Processing sheet with id=AO7, first strand: chain 'a' and resid 386 through 387 Processing sheet with id=AO8, first strand: chain 'a' and resid 405 through 406 Processing sheet with id=AO9, first strand: chain 'b' and resid 131 through 132 Processing sheet with id=AP1, first strand: chain 'b' and resid 143 through 147 Processing sheet with id=AP2, first strand: chain 'b' and resid 179 through 182 removed outlier: 3.988A pdb=" N GLY b 179 " --> pdb=" O ALA b 454 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'b' and resid 194 through 196 Processing sheet with id=AP4, first strand: chain 'b' and resid 260 through 261 Processing sheet with id=AP5, first strand: chain 'b' and resid 283 through 288 Processing sheet with id=AP6, first strand: chain 'b' and resid 314 through 316 Processing sheet with id=AP7, first strand: chain 'b' and resid 355 through 357 Processing sheet with id=AP8, first strand: chain 'b' and resid 386 through 387 Processing sheet with id=AP9, first strand: chain 'b' and resid 405 through 406 Processing sheet with id=AQ1, first strand: chain 'c' and resid 143 through 147 Processing sheet with id=AQ2, first strand: chain 'c' and resid 194 through 196 Processing sheet with id=AQ3, first strand: chain 'c' and resid 260 through 261 Processing sheet with id=AQ4, first strand: chain 'c' and resid 283 through 288 Processing sheet with id=AQ5, first strand: chain 'c' and resid 314 through 315 removed outlier: 3.584A pdb=" N ASN c 324 " --> pdb=" O TYR c 314 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'c' and resid 355 through 357 Processing sheet with id=AQ7, first strand: chain 'c' and resid 386 through 387 Processing sheet with id=AQ8, first strand: chain 'c' and resid 405 through 406 Processing sheet with id=AQ9, first strand: chain 'd' and resid 143 through 147 Processing sheet with id=AR1, first strand: chain 'd' and resid 181 through 182 removed outlier: 4.640A pdb=" N THR d 181 " --> pdb=" O SER d 452 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER d 452 " --> pdb=" O THR d 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR1 Processing sheet with id=AR2, first strand: chain 'd' and resid 194 through 196 Processing sheet with id=AR3, first strand: chain 'd' and resid 260 through 261 removed outlier: 3.542A pdb=" N ALA d 261 " --> pdb=" O MET d 367 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'd' and resid 283 through 288 Processing sheet with id=AR5, first strand: chain 'd' and resid 314 through 315 removed outlier: 3.508A pdb=" N ASN d 324 " --> pdb=" O TYR d 314 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'd' and resid 355 through 357 Processing sheet with id=AR7, first strand: chain 'd' and resid 382 through 383 Processing sheet with id=AR8, first strand: chain 'd' and resid 386 through 387 Processing sheet with id=AR9, first strand: chain 'd' and resid 405 through 406 Processing sheet with id=AS1, first strand: chain 'e' and resid 143 through 147 Processing sheet with id=AS2, first strand: chain 'e' and resid 194 through 196 Processing sheet with id=AS3, first strand: chain 'e' and resid 260 through 263 removed outlier: 5.542A pdb=" N SER e 263 " --> pdb=" O ALA e 365 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA e 365 " --> pdb=" O SER e 263 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'e' and resid 283 through 288 Processing sheet with id=AS5, first strand: chain 'e' and resid 314 through 315 Processing sheet with id=AS6, first strand: chain 'e' and resid 386 through 387 Processing sheet with id=AS7, first strand: chain 'e' and resid 405 through 406 Processing sheet with id=AS8, first strand: chain 'f' and resid 143 through 147 Processing sheet with id=AS9, first strand: chain 'f' and resid 181 through 182 removed outlier: 3.521A pdb=" N SER f 452 " --> pdb=" O THR f 181 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'f' and resid 194 through 196 Processing sheet with id=AT2, first strand: chain 'f' and resid 260 through 261 Processing sheet with id=AT3, first strand: chain 'f' and resid 283 through 288 Processing sheet with id=AT4, first strand: chain 'f' and resid 314 through 316 Processing sheet with id=AT5, first strand: chain 'f' and resid 355 through 357 Processing sheet with id=AT6, first strand: chain 'f' and resid 386 through 387 Processing sheet with id=AT7, first strand: chain 'f' and resid 405 through 406 Processing sheet with id=AT8, first strand: chain 'g' and resid 131 through 132 Processing sheet with id=AT9, first strand: chain 'g' and resid 143 through 147 Processing sheet with id=AU1, first strand: chain 'g' and resid 179 through 182 removed outlier: 3.878A pdb=" N GLY g 179 " --> pdb=" O ALA g 454 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'g' and resid 194 through 196 Processing sheet with id=AU3, first strand: chain 'g' and resid 283 through 288 Processing sheet with id=AU4, first strand: chain 'g' and resid 314 through 315 removed outlier: 3.604A pdb=" N ASN g 324 " --> pdb=" O TYR g 314 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'g' and resid 355 through 357 Processing sheet with id=AU6, first strand: chain 'g' and resid 386 through 387 Processing sheet with id=AU7, first strand: chain 'g' and resid 405 through 406 Processing sheet with id=AU8, first strand: chain 'h' and resid 131 through 132 Processing sheet with id=AU9, first strand: chain 'h' and resid 143 through 147 Processing sheet with id=AV1, first strand: chain 'h' and resid 194 through 196 Processing sheet with id=AV2, first strand: chain 'h' and resid 260 through 261 Processing sheet with id=AV3, first strand: chain 'h' and resid 283 through 288 Processing sheet with id=AV4, first strand: chain 'h' and resid 314 through 315 removed outlier: 3.713A pdb=" N ASN h 324 " --> pdb=" O TYR h 314 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'h' and resid 355 through 357 Processing sheet with id=AV6, first strand: chain 'h' and resid 386 through 387 Processing sheet with id=AV7, first strand: chain 'h' and resid 405 through 406 5083 hydrogen bonds defined for protein. 14637 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: 42.45 Time building geometry restraints manager: 32.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 29366 1.33 - 1.46: 11613 1.46 - 1.58: 49868 1.58 - 1.70: 3 1.70 - 1.82: 276 Bond restraints: 91126 Sorted by residual: bond pdb=" C ASP E 316 " pdb=" O ASP E 316 " ideal model delta sigma weight residual 1.236 1.267 -0.031 7.30e-03 1.88e+04 1.75e+01 bond pdb=" CA GLY C 179 " pdb=" C GLY C 179 " ideal model delta sigma weight residual 1.520 1.550 -0.030 7.30e-03 1.88e+04 1.67e+01 bond pdb=" CB PRO O 416 " pdb=" CG PRO O 416 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.97e+00 bond pdb=" CG LEU D 492 " pdb=" CD1 LEU D 492 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.22e+00 bond pdb=" CB PRO c 416 " pdb=" CG PRO c 416 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.99e+00 ... (remaining 91121 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.30: 629 105.30 - 111.63: 43694 111.63 - 117.97: 26797 117.97 - 124.30: 52157 124.30 - 130.63: 601 Bond angle restraints: 123878 Sorted by residual: angle pdb=" CA PRO O 416 " pdb=" N PRO O 416 " pdb=" CD PRO O 416 " ideal model delta sigma weight residual 112.00 101.92 10.08 1.40e+00 5.10e-01 5.19e+01 angle pdb=" N ILE b 289 " pdb=" CA ILE b 289 " pdb=" C ILE b 289 " ideal model delta sigma weight residual 112.29 106.93 5.36 9.40e-01 1.13e+00 3.25e+01 angle pdb=" CA PRO c 416 " pdb=" N PRO c 416 " pdb=" CD PRO c 416 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" N ILE B 5 " pdb=" CA ILE B 5 " pdb=" C ILE B 5 " ideal model delta sigma weight residual 106.21 110.86 -4.65 1.07e+00 8.73e-01 1.89e+01 angle pdb=" C GLY E 169 " pdb=" N LEU E 170 " pdb=" CA LEU E 170 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 ... (remaining 123873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 50922 17.98 - 35.96: 3707 35.96 - 53.94: 536 53.94 - 71.92: 191 71.92 - 89.90: 51 Dihedral angle restraints: 55407 sinusoidal: 19504 harmonic: 35903 Sorted by residual: dihedral pdb=" CA VAL d 538 " pdb=" C VAL d 538 " pdb=" N PRO d 539 " pdb=" CA PRO d 539 " ideal model delta harmonic sigma weight residual -180.00 -147.35 -32.65 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA ASN D 176 " pdb=" C ASN D 176 " pdb=" N GLY D 177 " pdb=" CA GLY D 177 " ideal model delta harmonic sigma weight residual 180.00 -152.88 -27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ILE K 5 " pdb=" C ILE K 5 " pdb=" N ASN K 6 " pdb=" CA ASN K 6 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 55404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 13824 0.068 - 0.136: 1354 0.136 - 0.204: 64 0.204 - 0.272: 4 0.272 - 0.340: 3 Chirality restraints: 15249 Sorted by residual: chirality pdb=" CB THR L 457 " pdb=" CA THR L 457 " pdb=" OG1 THR L 457 " pdb=" CG2 THR L 457 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR D 457 " pdb=" CA THR D 457 " pdb=" OG1 THR D 457 " pdb=" CG2 THR D 457 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB THR N 457 " pdb=" CA THR N 457 " pdb=" OG1 THR N 457 " pdb=" CG2 THR N 457 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 15246 not shown) Planarity restraints: 16583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO c 415 " -0.085 5.00e-02 4.00e+02 1.24e-01 2.48e+01 pdb=" N PRO c 416 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO c 416 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO c 416 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO O 415 " 0.078 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO O 416 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO O 416 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO O 416 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO a 415 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO a 416 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO a 416 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO a 416 " -0.059 5.00e-02 4.00e+02 ... (remaining 16580 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1957 2.66 - 3.22: 95943 3.22 - 3.78: 141674 3.78 - 4.34: 176508 4.34 - 4.90: 291252 Nonbonded interactions: 707334 Sorted by model distance: nonbonded pdb=" OG SER h 258 " pdb=" O ILE h 369 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR I 234 " pdb=" OG1 THR I 384 " model vdw 2.107 2.440 nonbonded pdb=" OG1 THR F 234 " pdb=" OG1 THR F 384 " model vdw 2.107 2.440 nonbonded pdb=" OG SER C 258 " pdb=" O ILE C 369 " model vdw 2.112 2.440 nonbonded pdb=" OG SER B 258 " pdb=" O ILE B 369 " model vdw 2.122 2.440 ... (remaining 707329 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 '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' selection = chain 'O' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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 group one per residue 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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 14.990 Check model and map are aligned: 0.970 Set scattering table: 0.600 Process input model: 191.690 Find NCS groups from input model: 5.240 Set up NCS constraints: 0.680 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 222.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.003 0.141 91126 Z= 0.190 Angle : 0.631 11.867 123878 Z= 0.346 Chirality : 0.040 0.340 15249 Planarity : 0.004 0.124 16583 Dihedral : 13.406 89.897 32315 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.65 (0.08), residues: 12512 helix: 3.16 (0.07), residues: 5181 sheet: 0.55 (0.14), residues: 1357 loop : -2.30 (0.07), residues: 5974 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.001 PHE F 374 TYR 0.028 0.001 TYR O 252 ARG 0.013 0.001 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2316 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2309 time to evaluate : 9.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8460 (tt0) cc_final: 0.7982 (tp30) REVERT: A 174 ASN cc_start: 0.7934 (t0) cc_final: 0.7679 (t0) REVERT: A 349 GLN cc_start: 0.9061 (pp30) cc_final: 0.8850 (pp30) REVERT: A 358 ASP cc_start: 0.7320 (m-30) cc_final: 0.6472 (p0) REVERT: A 436 LYS cc_start: 0.8130 (mttt) cc_final: 0.7745 (mttp) REVERT: B 122 GLU cc_start: 0.8483 (tp30) cc_final: 0.7854 (tp30) REVERT: B 297 ASN cc_start: 0.8651 (m-40) cc_final: 0.8158 (m-40) REVERT: B 418 TYR cc_start: 0.8297 (m-80) cc_final: 0.7630 (m-80) REVERT: C 30 GLU cc_start: 0.7233 (tt0) cc_final: 0.6761 (tp30) REVERT: C 232 LYS cc_start: 0.7865 (mmmm) cc_final: 0.7651 (mmtm) REVERT: C 284 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8406 (tptp) REVERT: C 297 ASN cc_start: 0.8398 (m110) cc_final: 0.7734 (m-40) REVERT: C 447 THR cc_start: 0.9122 (t) cc_final: 0.8837 (p) REVERT: C 505 ARG cc_start: 0.7850 (ttm110) cc_final: 0.6969 (ttt180) REVERT: D 70 ASP cc_start: 0.7548 (m-30) cc_final: 0.7333 (m-30) REVERT: D 85 ILE cc_start: 0.8467 (mt) cc_final: 0.7956 (mt) REVERT: D 284 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8297 (ttpp) REVERT: D 358 ASP cc_start: 0.8441 (m-30) cc_final: 0.8028 (t0) REVERT: D 370 ASP cc_start: 0.8553 (t0) cc_final: 0.8272 (m-30) REVERT: D 381 ASP cc_start: 0.8628 (p0) cc_final: 0.8277 (p0) REVERT: D 449 ASP cc_start: 0.7970 (m-30) cc_final: 0.7760 (m-30) REVERT: D 451 THR cc_start: 0.9485 (m) cc_final: 0.9219 (p) REVERT: D 518 MET cc_start: 0.8410 (tmm) cc_final: 0.7987 (tpt) REVERT: D 537 GLN cc_start: 0.7863 (tp40) cc_final: 0.7298 (tt0) REVERT: E 105 SER cc_start: 0.8819 (t) cc_final: 0.8323 (t) REVERT: E 144 MET cc_start: 0.8317 (ttt) cc_final: 0.8032 (ttt) REVERT: E 465 ASP cc_start: 0.7998 (p0) cc_final: 0.7777 (t0) REVERT: F 16 ASN cc_start: 0.8339 (m-40) cc_final: 0.8133 (m-40) REVERT: F 18 ILE cc_start: 0.8747 (mt) cc_final: 0.8546 (tp) REVERT: F 122 GLU cc_start: 0.8445 (tp30) cc_final: 0.7570 (tp30) REVERT: F 151 ASN cc_start: 0.8735 (m-40) cc_final: 0.8487 (m-40) REVERT: F 284 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8022 (tmtt) REVERT: F 367 MET cc_start: 0.6677 (mpp) cc_final: 0.6208 (mmm) REVERT: F 380 ASN cc_start: 0.8248 (m-40) cc_final: 0.7784 (t0) REVERT: F 507 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8018 (mm-40) REVERT: G 84 GLU cc_start: 0.6979 (tt0) cc_final: 0.6715 (tt0) REVERT: G 122 GLU cc_start: 0.8974 (tp30) cc_final: 0.7704 (tp30) REVERT: G 436 LYS cc_start: 0.8356 (mppt) cc_final: 0.7240 (tptm) REVERT: G 453 LYS cc_start: 0.8346 (mttp) cc_final: 0.8071 (mttp) REVERT: H 168 LEU cc_start: 0.9133 (mp) cc_final: 0.8664 (tp) REVERT: H 315 MET cc_start: 0.5183 (mmm) cc_final: 0.3818 (mmp) REVERT: I 108 ASP cc_start: 0.8320 (m-30) cc_final: 0.8090 (m-30) REVERT: I 161 LYS cc_start: 0.8664 (mptt) cc_final: 0.8449 (mtmt) REVERT: I 350 THR cc_start: 0.7720 (p) cc_final: 0.7072 (p) REVERT: I 423 ASP cc_start: 0.7329 (p0) cc_final: 0.6913 (p0) REVERT: J 58 ILE cc_start: 0.8536 (pt) cc_final: 0.8234 (mt) REVERT: J 180 GLU cc_start: 0.6775 (tp30) cc_final: 0.6472 (tp30) REVERT: J 194 PHE cc_start: 0.7165 (t80) cc_final: 0.6564 (t80) REVERT: J 367 MET cc_start: 0.5892 (mpp) cc_final: 0.5487 (mpp) REVERT: J 484 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7038 (tpt170) REVERT: J 505 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.6999 (mtp-110) REVERT: K 114 ASP cc_start: 0.8913 (t0) cc_final: 0.8696 (m-30) REVERT: K 116 ILE cc_start: 0.9280 (mm) cc_final: 0.8873 (tp) REVERT: K 122 GLU cc_start: 0.7395 (tp30) cc_final: 0.6951 (mm-30) REVERT: K 265 ASP cc_start: 0.6681 (p0) cc_final: 0.6362 (t0) REVERT: K 372 ASN cc_start: 0.8691 (m110) cc_final: 0.8459 (t0) REVERT: K 406 MET cc_start: 0.5085 (tpt) cc_final: 0.3571 (ptm) REVERT: K 508 ASP cc_start: 0.6675 (m-30) cc_final: 0.6384 (m-30) REVERT: L 42 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8528 (pttt) REVERT: L 174 ASN cc_start: 0.9044 (t0) cc_final: 0.8529 (t0) REVERT: L 274 PHE cc_start: 0.7524 (t80) cc_final: 0.6671 (t80) REVERT: L 355 PHE cc_start: 0.6145 (m-10) cc_final: 0.5523 (m-10) REVERT: L 367 MET cc_start: 0.7659 (ppp) cc_final: 0.7428 (ppp) REVERT: L 380 ASN cc_start: 0.8719 (m110) cc_final: 0.8432 (p0) REVERT: L 518 MET cc_start: 0.8966 (tmm) cc_final: 0.8644 (ttt) REVERT: M 19 ASN cc_start: 0.8368 (m-40) cc_final: 0.7786 (t0) REVERT: M 20 LYS cc_start: 0.8529 (mppt) cc_final: 0.8324 (mptt) REVERT: M 36 LEU cc_start: 0.7439 (tp) cc_final: 0.7209 (tp) REVERT: M 122 GLU cc_start: 0.7614 (tp30) cc_final: 0.6343 (mt-10) REVERT: M 140 LYS cc_start: 0.8512 (ptpt) cc_final: 0.7635 (mttp) REVERT: M 314 TYR cc_start: 0.6178 (m-10) cc_final: 0.5784 (m-10) REVERT: M 351 ASP cc_start: 0.8802 (p0) cc_final: 0.8530 (t0) REVERT: M 380 ASN cc_start: 0.7587 (m110) cc_final: 0.6716 (t0) REVERT: M 421 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7808 (mm110) REVERT: M 472 ASP cc_start: 0.7462 (m-30) cc_final: 0.7191 (m-30) REVERT: M 482 GLN cc_start: 0.8593 (tt0) cc_final: 0.8312 (tt0) REVERT: N 405 TYR cc_start: 0.6542 (m-10) cc_final: 0.5932 (m-10) REVERT: N 423 ASP cc_start: 0.8826 (p0) cc_final: 0.8620 (p0) REVERT: N 507 GLN cc_start: 0.7701 (mm110) cc_final: 0.7435 (mm110) REVERT: O 88 ASN cc_start: 0.8600 (m-40) cc_final: 0.8209 (m110) REVERT: O 122 GLU cc_start: 0.8643 (tp30) cc_final: 0.7249 (mm-30) REVERT: O 544 SER cc_start: 0.8321 (p) cc_final: 0.8037 (p) REVERT: a 131 GLN cc_start: 0.8146 (pt0) cc_final: 0.7439 (pp30) REVERT: a 152 ASP cc_start: 0.7786 (m-30) cc_final: 0.7440 (p0) REVERT: a 220 ASP cc_start: 0.8042 (m-30) cc_final: 0.7781 (m-30) REVERT: a 234 THR cc_start: 0.4689 (p) cc_final: 0.3853 (p) REVERT: a 315 MET cc_start: 0.5456 (tpp) cc_final: 0.4623 (tmm) REVERT: a 367 MET cc_start: 0.5901 (mpp) cc_final: 0.5523 (mpp) REVERT: a 392 TYR cc_start: 0.5846 (m-80) cc_final: 0.5626 (m-80) REVERT: a 406 MET cc_start: 0.6469 (mmm) cc_final: 0.4630 (mtm) REVERT: a 436 LYS cc_start: 0.7517 (mttt) cc_final: 0.7219 (mptt) REVERT: a 511 TYR cc_start: 0.7268 (m-80) cc_final: 0.6797 (m-80) REVERT: a 537 GLN cc_start: 0.8351 (tp40) cc_final: 0.7697 (tp40) REVERT: b 40 SER cc_start: 0.6670 (p) cc_final: 0.6298 (m) REVERT: b 48 GLN cc_start: 0.8662 (tt0) cc_final: 0.8393 (tp40) REVERT: b 58 ILE cc_start: 0.8967 (pt) cc_final: 0.8729 (pt) REVERT: b 61 LEU cc_start: 0.8828 (mt) cc_final: 0.8584 (mt) REVERT: b 122 GLU cc_start: 0.8201 (tp30) cc_final: 0.7941 (tm-30) REVERT: b 141 ASP cc_start: 0.7635 (m-30) cc_final: 0.7229 (p0) REVERT: b 180 GLU cc_start: 0.5200 (tp30) cc_final: 0.4686 (pt0) REVERT: c 69 ASN cc_start: 0.9028 (m110) cc_final: 0.8788 (m110) REVERT: c 122 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8453 (tm-30) REVERT: c 392 TYR cc_start: 0.7831 (m-80) cc_final: 0.7474 (m-80) REVERT: c 426 ILE cc_start: 0.7967 (mt) cc_final: 0.7649 (mt) REVERT: c 541 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8126 (tp40) REVERT: d 66 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8204 (mtt90) REVERT: d 122 GLU cc_start: 0.8681 (tp30) cc_final: 0.8467 (tp30) REVERT: d 189 LYS cc_start: 0.8320 (pptt) cc_final: 0.7966 (pttt) REVERT: d 299 ASP cc_start: 0.7985 (p0) cc_final: 0.7467 (t0) REVERT: d 315 MET cc_start: 0.6778 (tpt) cc_final: 0.6028 (tmm) REVERT: d 372 ASN cc_start: 0.8196 (m-40) cc_final: 0.7951 (t0) REVERT: d 436 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7649 (tttt) REVERT: d 453 LYS cc_start: 0.7542 (tmmt) cc_final: 0.7204 (mttt) REVERT: d 491 ASN cc_start: 0.9106 (t0) cc_final: 0.8552 (t0) REVERT: e 42 LYS cc_start: 0.7756 (tptt) cc_final: 0.7265 (tmmt) REVERT: e 50 ILE cc_start: 0.8837 (mm) cc_final: 0.8593 (mm) REVERT: e 151 ASN cc_start: 0.8470 (m-40) cc_final: 0.8039 (m-40) REVERT: e 211 ASP cc_start: 0.7501 (m-30) cc_final: 0.7100 (t70) REVERT: e 271 LEU cc_start: 0.7572 (mm) cc_final: 0.7355 (mm) REVERT: e 315 MET cc_start: 0.7090 (tpp) cc_final: 0.6347 (mtm) REVERT: e 501 GLU cc_start: 0.8177 (tt0) cc_final: 0.7575 (tp30) REVERT: f 15 GLN cc_start: 0.8125 (mt0) cc_final: 0.7878 (mm110) REVERT: f 278 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5589 (mt0) REVERT: f 314 TYR cc_start: 0.6817 (m-80) cc_final: 0.6469 (m-80) REVERT: f 501 GLU cc_start: 0.8892 (tp30) cc_final: 0.8407 (tp30) REVERT: f 505 ARG cc_start: 0.8898 (ttm-80) cc_final: 0.7836 (ttt180) REVERT: g 87 ASN cc_start: 0.7232 (m110) cc_final: 0.6967 (m-40) REVERT: g 144 MET cc_start: 0.8109 (ttt) cc_final: 0.7718 (ttt) REVERT: g 250 TYR cc_start: 0.5786 (m-80) cc_final: 0.5509 (m-80) REVERT: g 367 MET cc_start: 0.5353 (mpp) cc_final: 0.4920 (mtt) REVERT: g 411 LEU cc_start: 0.7923 (tp) cc_final: 0.7717 (tp) REVERT: g 447 THR cc_start: 0.7936 (p) cc_final: 0.7709 (p) REVERT: h 19 ASN cc_start: 0.8610 (m110) cc_final: 0.8352 (p0) REVERT: h 168 LEU cc_start: 0.8976 (mt) cc_final: 0.8767 (mt) REVERT: h 367 MET cc_start: 0.8916 (mpp) cc_final: 0.8314 (mpp) REVERT: h 445 LYS cc_start: 0.8606 (mptt) cc_final: 0.7708 (tttt) outliers start: 7 outliers final: 0 residues processed: 2316 average time/residue: 0.7624 time to fit residues: 3119.5071 Evaluate side-chains 1567 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1567 time to evaluate : 7.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1048 optimal weight: 20.0000 chunk 941 optimal weight: 20.0000 chunk 522 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 635 optimal weight: 0.0870 chunk 502 optimal weight: 0.9990 chunk 973 optimal weight: 7.9990 chunk 376 optimal weight: 4.9990 chunk 591 optimal weight: 7.9990 chunk 724 optimal weight: 8.9990 chunk 1127 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 39 ASN A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 16 ASN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 183 ASN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** G 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 376 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 331 GLN K 522 GLN L 63 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN N 376 ASN N 482 GLN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 86 ASN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 507 GLN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 231 ASN b 294 GLN b 331 GLN ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 GLN ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN d 349 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 529 ASN f 90 GLN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 278 GLN ** f 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 ASN ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN g 90 GLN ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 ASN h 19 ASN ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 113 GLN ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN h 541 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 91126 Z= 0.248 Angle : 0.608 10.071 123878 Z= 0.331 Chirality : 0.040 0.244 15249 Planarity : 0.003 0.074 16583 Dihedral : 4.720 31.372 13110 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.23 % Allowed : 5.01 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.56 (0.08), residues: 12512 helix: 3.00 (0.07), residues: 5337 sheet: 0.37 (0.13), residues: 1357 loop : -2.38 (0.07), residues: 5818 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE L 173 TYR 0.019 0.002 TYR b 252 ARG 0.009 0.001 ARG g 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1958 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1936 time to evaluate : 7.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8551 (tt0) cc_final: 0.7933 (tp30) REVERT: A 95 LEU cc_start: 0.9100 (mt) cc_final: 0.8702 (mp) REVERT: A 349 GLN cc_start: 0.9116 (pp30) cc_final: 0.8875 (pp30) REVERT: A 358 ASP cc_start: 0.7321 (m-30) cc_final: 0.6447 (p0) REVERT: A 392 TYR cc_start: 0.8826 (m-10) cc_final: 0.8594 (m-10) REVERT: A 394 VAL cc_start: 0.7877 (t) cc_final: 0.7444 (p) REVERT: A 536 ASN cc_start: 0.8154 (m110) cc_final: 0.7462 (t0) REVERT: B 39 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8098 (m-40) REVERT: B 105 SER cc_start: 0.8901 (t) cc_final: 0.8675 (t) REVERT: B 122 GLU cc_start: 0.8682 (tp30) cc_final: 0.7873 (tp30) REVERT: C 30 GLU cc_start: 0.7402 (tt0) cc_final: 0.6883 (tp30) REVERT: C 367 MET cc_start: 0.7825 (mpp) cc_final: 0.7569 (mpp) REVERT: C 447 THR cc_start: 0.9221 (t) cc_final: 0.8931 (p) REVERT: C 505 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7024 (ttt180) REVERT: D 10 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8096 (pp) REVERT: D 121 ASP cc_start: 0.8211 (t70) cc_final: 0.7765 (t0) REVERT: D 154 GLN cc_start: 0.7524 (mt0) cc_final: 0.7177 (mt0) REVERT: D 284 LYS cc_start: 0.9007 (mmtm) cc_final: 0.8702 (ttpp) REVERT: D 358 ASP cc_start: 0.8338 (m-30) cc_final: 0.7974 (t0) REVERT: D 381 ASP cc_start: 0.8687 (p0) cc_final: 0.8236 (p0) REVERT: D 537 GLN cc_start: 0.8046 (tp40) cc_final: 0.7344 (tt0) REVERT: E 144 MET cc_start: 0.8493 (ttt) cc_final: 0.7699 (ttt) REVERT: E 209 TYR cc_start: 0.8300 (m-80) cc_final: 0.7242 (m-80) REVERT: E 363 ASP cc_start: 0.6014 (m-30) cc_final: 0.5483 (t70) REVERT: F 122 GLU cc_start: 0.8355 (tp30) cc_final: 0.7594 (tp30) REVERT: F 151 ASN cc_start: 0.8760 (m-40) cc_final: 0.8501 (m-40) REVERT: F 219 VAL cc_start: 0.8693 (p) cc_final: 0.8359 (p) REVERT: F 232 LYS cc_start: 0.8535 (mppt) cc_final: 0.8301 (mppt) REVERT: F 283 THR cc_start: 0.8519 (p) cc_final: 0.8304 (p) REVERT: F 284 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8021 (tmtt) REVERT: F 380 ASN cc_start: 0.8293 (m-40) cc_final: 0.7720 (t0) REVERT: G 436 LYS cc_start: 0.8503 (mppt) cc_final: 0.7958 (ptmm) REVERT: G 439 TYR cc_start: 0.8379 (m-80) cc_final: 0.8044 (m-80) REVERT: H 131 GLN cc_start: 0.8557 (pp30) cc_final: 0.8346 (pt0) REVERT: H 168 LEU cc_start: 0.9227 (mp) cc_final: 0.8783 (tp) REVERT: H 315 MET cc_start: 0.5634 (mmm) cc_final: 0.4485 (mmp) REVERT: H 423 ASP cc_start: 0.7716 (p0) cc_final: 0.7463 (p0) REVERT: I 32 LEU cc_start: 0.8298 (mm) cc_final: 0.8050 (mm) REVERT: I 161 LYS cc_start: 0.8802 (mptt) cc_final: 0.8380 (mtmt) REVERT: I 419 TYR cc_start: 0.7049 (m-80) cc_final: 0.6787 (m-10) REVERT: I 423 ASP cc_start: 0.7512 (p0) cc_final: 0.6999 (p0) REVERT: J 58 ILE cc_start: 0.8523 (pt) cc_final: 0.8285 (mt) REVERT: J 59 LYS cc_start: 0.7252 (mttm) cc_final: 0.6797 (tmtt) REVERT: J 180 GLU cc_start: 0.6667 (tp30) cc_final: 0.6356 (tp30) REVERT: J 367 MET cc_start: 0.5920 (mpp) cc_final: 0.5415 (mpp) REVERT: K 16 ASN cc_start: 0.8501 (m110) cc_final: 0.8000 (m110) REVERT: K 89 LEU cc_start: 0.8997 (mm) cc_final: 0.8764 (mm) REVERT: K 114 ASP cc_start: 0.9051 (t0) cc_final: 0.8723 (m-30) REVERT: K 116 ILE cc_start: 0.9359 (mm) cc_final: 0.8945 (tp) REVERT: K 122 GLU cc_start: 0.7380 (tp30) cc_final: 0.6983 (mm-30) REVERT: K 144 MET cc_start: 0.8435 (tpp) cc_final: 0.7660 (ttm) REVERT: K 372 ASN cc_start: 0.8693 (m110) cc_final: 0.8439 (t0) REVERT: K 406 MET cc_start: 0.5041 (tpt) cc_final: 0.3597 (ptm) REVERT: K 508 ASP cc_start: 0.6813 (m-30) cc_final: 0.6519 (m-30) REVERT: L 19 ASN cc_start: 0.8512 (m-40) cc_final: 0.7860 (t0) REVERT: L 355 PHE cc_start: 0.6239 (m-10) cc_final: 0.5679 (m-80) REVERT: L 380 ASN cc_start: 0.8822 (m110) cc_final: 0.8512 (p0) REVERT: M 19 ASN cc_start: 0.8496 (m-40) cc_final: 0.7812 (t0) REVERT: M 122 GLU cc_start: 0.7710 (tp30) cc_final: 0.6708 (mt-10) REVERT: M 140 LYS cc_start: 0.8587 (ptpt) cc_final: 0.7710 (mttp) REVERT: M 331 GLN cc_start: 0.6213 (tp-100) cc_final: 0.4799 (mp10) REVERT: M 351 ASP cc_start: 0.8845 (p0) cc_final: 0.8525 (t0) REVERT: M 472 ASP cc_start: 0.7529 (m-30) cc_final: 0.7276 (m-30) REVERT: M 482 GLN cc_start: 0.8729 (tt0) cc_final: 0.8482 (tt0) REVERT: M 525 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8342 (tp40) REVERT: N 140 LYS cc_start: 0.8293 (mttt) cc_final: 0.7976 (mttp) REVERT: N 217 SER cc_start: 0.7555 (t) cc_final: 0.7345 (p) REVERT: N 220 ASP cc_start: 0.8640 (m-30) cc_final: 0.8199 (m-30) REVERT: N 405 TYR cc_start: 0.7031 (m-80) cc_final: 0.6638 (m-10) REVERT: N 451 THR cc_start: 0.8892 (m) cc_final: 0.8479 (m) REVERT: O 42 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7920 (mtmt) REVERT: O 88 ASN cc_start: 0.8659 (m-40) cc_final: 0.8425 (t0) REVERT: O 122 GLU cc_start: 0.8372 (tp30) cc_final: 0.7129 (mm-30) REVERT: O 123 ILE cc_start: 0.8435 (mt) cc_final: 0.7487 (mt) REVERT: O 159 ASP cc_start: 0.8101 (p0) cc_final: 0.7798 (p0) REVERT: O 344 LYS cc_start: 0.6944 (tptm) cc_final: 0.6569 (tptp) REVERT: a 110 ASP cc_start: 0.7877 (m-30) cc_final: 0.7652 (m-30) REVERT: a 115 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7745 (tp30) REVERT: a 152 ASP cc_start: 0.7859 (m-30) cc_final: 0.7368 (p0) REVERT: a 234 THR cc_start: 0.4918 (p) cc_final: 0.4406 (p) REVERT: a 241 PHE cc_start: 0.7523 (m-80) cc_final: 0.7279 (m-80) REVERT: a 252 TYR cc_start: 0.6767 (m-80) cc_final: 0.6195 (m-80) REVERT: a 265 ASP cc_start: 0.6640 (p0) cc_final: 0.6406 (p0) REVERT: a 315 MET cc_start: 0.5145 (tpp) cc_final: 0.4846 (tmm) REVERT: a 392 TYR cc_start: 0.6188 (m-80) cc_final: 0.5812 (m-80) REVERT: a 418 TYR cc_start: 0.5654 (m-10) cc_final: 0.5437 (m-10) REVERT: a 436 LYS cc_start: 0.7810 (mttt) cc_final: 0.7353 (mptt) REVERT: b 40 SER cc_start: 0.6732 (p) cc_final: 0.6380 (m) REVERT: b 58 ILE cc_start: 0.8953 (pt) cc_final: 0.8739 (pt) REVERT: b 61 LEU cc_start: 0.8865 (mt) cc_final: 0.8562 (mt) REVERT: b 66 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8211 (tpp80) REVERT: b 122 GLU cc_start: 0.8493 (tp30) cc_final: 0.8060 (tm-30) REVERT: b 141 ASP cc_start: 0.7796 (m-30) cc_final: 0.7262 (p0) REVERT: b 431 ASP cc_start: 0.8572 (p0) cc_final: 0.8319 (p0) REVERT: c 79 GLU cc_start: 0.8430 (tp30) cc_final: 0.7935 (tp30) REVERT: c 106 ASP cc_start: 0.7826 (m-30) cc_final: 0.7589 (m-30) REVERT: c 144 MET cc_start: 0.7946 (ttt) cc_final: 0.7348 (ttt) REVERT: c 392 TYR cc_start: 0.7857 (m-80) cc_final: 0.7419 (m-80) REVERT: c 484 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6934 (ttp-170) REVERT: c 541 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8284 (tp40) REVERT: d 66 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8280 (mtt90) REVERT: d 122 GLU cc_start: 0.8832 (tp30) cc_final: 0.8401 (tp30) REVERT: d 189 LYS cc_start: 0.8279 (pptt) cc_final: 0.7830 (pttt) REVERT: d 299 ASP cc_start: 0.8055 (p0) cc_final: 0.7533 (t0) REVERT: d 315 MET cc_start: 0.6535 (tpt) cc_final: 0.5752 (tmm) REVERT: d 372 ASN cc_start: 0.8319 (m-40) cc_final: 0.8001 (t0) REVERT: d 453 LYS cc_start: 0.7663 (tmmt) cc_final: 0.7234 (mttt) REVERT: e 17 ASN cc_start: 0.7645 (m110) cc_final: 0.7298 (m110) REVERT: e 42 LYS cc_start: 0.7859 (tptt) cc_final: 0.7336 (tmmt) REVERT: e 50 ILE cc_start: 0.8977 (mm) cc_final: 0.8583 (mm) REVERT: e 129 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7623 (mm-40) REVERT: e 211 ASP cc_start: 0.7668 (m-30) cc_final: 0.7261 (t70) REVERT: e 212 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7065 (tptp) REVERT: e 271 LEU cc_start: 0.7675 (mm) cc_final: 0.7237 (mm) REVERT: e 468 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8582 (mp) REVERT: e 501 GLU cc_start: 0.8119 (tt0) cc_final: 0.7784 (tp30) REVERT: e 514 GLU cc_start: 0.8102 (tp30) cc_final: 0.7895 (tp30) REVERT: f 15 GLN cc_start: 0.8226 (mt0) cc_final: 0.7998 (mm110) REVERT: f 122 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8249 (mm-30) REVERT: f 232 LYS cc_start: 0.7910 (tptp) cc_final: 0.7261 (mttm) REVERT: f 278 GLN cc_start: 0.6053 (mm110) cc_final: 0.5825 (mt0) REVERT: f 314 TYR cc_start: 0.6763 (m-80) cc_final: 0.5986 (m-80) REVERT: f 501 GLU cc_start: 0.8892 (tp30) cc_final: 0.8440 (tp30) REVERT: f 518 MET cc_start: 0.8073 (ppp) cc_final: 0.7836 (ppp) REVERT: g 87 ASN cc_start: 0.7538 (m110) cc_final: 0.7266 (m-40) REVERT: g 144 MET cc_start: 0.8749 (ttt) cc_final: 0.8355 (ttt) REVERT: g 235 THR cc_start: 0.7738 (p) cc_final: 0.7331 (t) REVERT: g 250 TYR cc_start: 0.5830 (m-80) cc_final: 0.5470 (m-80) REVERT: g 367 MET cc_start: 0.5510 (mpp) cc_final: 0.4991 (mtt) REVERT: h 168 LEU cc_start: 0.9086 (mt) cc_final: 0.8834 (mt) REVERT: h 367 MET cc_start: 0.8766 (mpp) cc_final: 0.8081 (mpp) REVERT: h 445 LYS cc_start: 0.8742 (mptt) cc_final: 0.7889 (tttm) outliers start: 22 outliers final: 5 residues processed: 1954 average time/residue: 0.7502 time to fit residues: 2644.4833 Evaluate side-chains 1454 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1446 time to evaluate : 7.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 626 optimal weight: 30.0000 chunk 350 optimal weight: 0.9980 chunk 938 optimal weight: 9.9990 chunk 768 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 chunk 1129 optimal weight: 4.9990 chunk 1220 optimal weight: 10.0000 chunk 1006 optimal weight: 4.9990 chunk 1120 optimal weight: 0.2980 chunk 385 optimal weight: 5.9990 chunk 906 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 17 ASN A 39 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN B 529 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN F 15 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN G 525 GLN G 529 ASN H 3 GLN H 52 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 GLN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN K 86 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 522 GLN L 52 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN ** N 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN ** O 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 ASN ** O 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 6 ASN a 22 GLN a 86 ASN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 GLN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 525 GLN ** b 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 GLN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN d 349 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 19 ASN f 98 GLN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 GLN g 98 GLN g 278 GLN ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 541 GLN ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 39 ASN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 91126 Z= 0.234 Angle : 0.590 11.201 123878 Z= 0.321 Chirality : 0.040 0.296 15249 Planarity : 0.003 0.060 16583 Dihedral : 4.745 27.662 13110 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % 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: 0.46 (0.08), residues: 12512 helix: 2.95 (0.07), residues: 5376 sheet: 0.20 (0.13), residues: 1321 loop : -2.46 (0.07), residues: 5815 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE F 173 TYR 0.022 0.002 TYR H 252 ARG 0.007 0.001 ARG f 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1914 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1906 time to evaluate : 7.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8523 (tt0) cc_final: 0.7951 (tp30) REVERT: A 115 GLU cc_start: 0.8538 (tt0) cc_final: 0.8253 (tt0) REVERT: A 171 ASN cc_start: 0.7709 (t0) cc_final: 0.7508 (t0) REVERT: A 349 GLN cc_start: 0.9089 (pp30) cc_final: 0.8850 (pp30) REVERT: A 358 ASP cc_start: 0.7573 (m-30) cc_final: 0.6398 (p0) REVERT: A 362 PHE cc_start: 0.7837 (m-80) cc_final: 0.7486 (m-80) REVERT: A 394 VAL cc_start: 0.7870 (t) cc_final: 0.7446 (p) REVERT: A 408 ASN cc_start: 0.9018 (p0) cc_final: 0.8814 (p0) REVERT: A 436 LYS cc_start: 0.8265 (mttt) cc_final: 0.7815 (mttp) REVERT: A 536 ASN cc_start: 0.8212 (m110) cc_final: 0.7466 (t0) REVERT: B 105 SER cc_start: 0.8852 (t) cc_final: 0.8589 (t) REVERT: B 122 GLU cc_start: 0.8760 (tp30) cc_final: 0.8048 (tp30) REVERT: B 406 MET cc_start: 0.8472 (tpt) cc_final: 0.8247 (tpp) REVERT: C 30 GLU cc_start: 0.7389 (tt0) cc_final: 0.6957 (tp30) REVERT: C 276 ASN cc_start: 0.8499 (m110) cc_final: 0.8256 (m110) REVERT: C 297 ASN cc_start: 0.8748 (m110) cc_final: 0.8082 (t0) REVERT: C 447 THR cc_start: 0.9221 (t) cc_final: 0.8993 (p) REVERT: C 505 ARG cc_start: 0.7959 (ttm110) cc_final: 0.7019 (ttt180) REVERT: D 30 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 121 ASP cc_start: 0.8206 (t70) cc_final: 0.7738 (t0) REVERT: D 284 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8599 (ttpp) REVERT: D 358 ASP cc_start: 0.8291 (m-30) cc_final: 0.7940 (t0) REVERT: D 370 ASP cc_start: 0.8583 (t0) cc_final: 0.8322 (m-30) REVERT: D 381 ASP cc_start: 0.8715 (p0) cc_final: 0.8287 (p0) REVERT: D 423 ASP cc_start: 0.8265 (p0) cc_final: 0.7887 (t0) REVERT: D 537 GLN cc_start: 0.7966 (tp40) cc_final: 0.7296 (tt0) REVERT: E 30 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8238 (tm-30) REVERT: E 34 SER cc_start: 0.9091 (t) cc_final: 0.8891 (p) REVERT: E 144 MET cc_start: 0.8607 (ttt) cc_final: 0.7983 (ttm) REVERT: E 265 ASP cc_start: 0.5197 (p0) cc_final: 0.4872 (p0) REVERT: E 363 ASP cc_start: 0.6019 (m-30) cc_final: 0.5420 (t70) REVERT: E 406 MET cc_start: 0.7520 (mtm) cc_final: 0.7065 (mtt) REVERT: F 44 ASP cc_start: 0.7775 (m-30) cc_final: 0.7176 (p0) REVERT: F 122 GLU cc_start: 0.8352 (tp30) cc_final: 0.7569 (tp30) REVERT: F 151 ASN cc_start: 0.8695 (m-40) cc_final: 0.8418 (m-40) REVERT: F 232 LYS cc_start: 0.8600 (mppt) cc_final: 0.8283 (mppt) REVERT: F 284 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8061 (tmtt) REVERT: F 380 ASN cc_start: 0.8237 (m-40) cc_final: 0.7728 (t0) REVERT: G 144 MET cc_start: 0.8472 (ttt) cc_final: 0.8179 (ttm) REVERT: G 209 TYR cc_start: 0.7863 (m-10) cc_final: 0.7518 (m-10) REVERT: G 436 LYS cc_start: 0.8432 (mppt) cc_final: 0.7886 (ptmt) REVERT: G 439 TYR cc_start: 0.8423 (m-80) cc_final: 0.7884 (m-80) REVERT: G 492 LEU cc_start: 0.9226 (tp) cc_final: 0.8924 (tp) REVERT: H 131 GLN cc_start: 0.8651 (pp30) cc_final: 0.8356 (pp30) REVERT: H 168 LEU cc_start: 0.9252 (mp) cc_final: 0.8817 (tp) REVERT: H 315 MET cc_start: 0.5603 (mmm) cc_final: 0.4669 (mmp) REVERT: H 423 ASP cc_start: 0.7833 (p0) cc_final: 0.7523 (p0) REVERT: I 32 LEU cc_start: 0.8216 (mm) cc_final: 0.7991 (mm) REVERT: I 108 ASP cc_start: 0.8516 (m-30) cc_final: 0.8276 (m-30) REVERT: I 122 GLU cc_start: 0.8570 (tp30) cc_final: 0.8250 (tp30) REVERT: I 161 LYS cc_start: 0.8872 (mptt) cc_final: 0.8474 (mtmt) REVERT: I 232 LYS cc_start: 0.7954 (pttp) cc_final: 0.7722 (pttm) REVERT: I 294 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7409 (tm-30) REVERT: I 406 MET cc_start: 0.4156 (mmm) cc_final: 0.3799 (tpt) REVERT: I 418 TYR cc_start: 0.8340 (m-10) cc_final: 0.7898 (m-10) REVERT: I 419 TYR cc_start: 0.7141 (m-80) cc_final: 0.6886 (m-10) REVERT: I 423 ASP cc_start: 0.7635 (p0) cc_final: 0.7116 (p0) REVERT: J 58 ILE cc_start: 0.8493 (pt) cc_final: 0.8166 (mt) REVERT: J 59 LYS cc_start: 0.7161 (mttm) cc_final: 0.6692 (tmtt) REVERT: J 314 TYR cc_start: 0.6448 (m-80) cc_final: 0.6205 (m-80) REVERT: J 367 MET cc_start: 0.5668 (mpp) cc_final: 0.5114 (mpp) REVERT: K 89 LEU cc_start: 0.9027 (mm) cc_final: 0.8721 (mm) REVERT: K 114 ASP cc_start: 0.9037 (t0) cc_final: 0.8771 (m-30) REVERT: K 372 ASN cc_start: 0.8683 (m110) cc_final: 0.8402 (t0) REVERT: K 406 MET cc_start: 0.4884 (tpt) cc_final: 0.3475 (ptm) REVERT: K 410 VAL cc_start: 0.8196 (p) cc_final: 0.7738 (p) REVERT: K 540 GLN cc_start: 0.8878 (pm20) cc_final: 0.8672 (pm20) REVERT: K 547 GLN cc_start: 0.6970 (pp30) cc_final: 0.6532 (pp30) REVERT: L 19 ASN cc_start: 0.8525 (m-40) cc_final: 0.7882 (t0) REVERT: L 274 PHE cc_start: 0.7381 (t80) cc_final: 0.6416 (t80) REVERT: L 367 MET cc_start: 0.7864 (ppp) cc_final: 0.6213 (tpp) REVERT: L 372 ASN cc_start: 0.7886 (m-40) cc_final: 0.7363 (p0) REVERT: L 501 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7761 (mm-30) REVERT: M 19 ASN cc_start: 0.8631 (m-40) cc_final: 0.7812 (t0) REVERT: M 122 GLU cc_start: 0.7887 (tp30) cc_final: 0.6735 (mt-10) REVERT: M 140 LYS cc_start: 0.8513 (ptpt) cc_final: 0.7763 (mttp) REVERT: M 351 ASP cc_start: 0.8821 (p0) cc_final: 0.8435 (t0) REVERT: M 482 GLN cc_start: 0.8726 (tt0) cc_final: 0.8401 (tt0) REVERT: M 525 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8351 (tp40) REVERT: M 537 GLN cc_start: 0.8444 (mp10) cc_final: 0.8015 (mp10) REVERT: N 140 LYS cc_start: 0.8379 (mttt) cc_final: 0.8040 (mttp) REVERT: N 180 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7809 (mm-30) REVERT: N 217 SER cc_start: 0.7874 (t) cc_final: 0.7532 (p) REVERT: N 220 ASP cc_start: 0.8745 (m-30) cc_final: 0.8239 (m-30) REVERT: N 405 TYR cc_start: 0.7057 (m-80) cc_final: 0.6605 (m-80) REVERT: O 42 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8129 (ttmt) REVERT: O 88 ASN cc_start: 0.8841 (m-40) cc_final: 0.8469 (t0) REVERT: O 122 GLU cc_start: 0.8404 (tp30) cc_final: 0.7082 (mm-30) REVERT: O 123 ILE cc_start: 0.8429 (mt) cc_final: 0.7501 (mt) REVERT: O 159 ASP cc_start: 0.8228 (p0) cc_final: 0.7912 (p0) REVERT: O 344 LYS cc_start: 0.6996 (tptm) cc_final: 0.6745 (tptm) REVERT: a 115 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7718 (tp30) REVERT: a 234 THR cc_start: 0.5009 (p) cc_final: 0.4439 (p) REVERT: a 252 TYR cc_start: 0.6785 (m-80) cc_final: 0.6238 (m-80) REVERT: a 392 TYR cc_start: 0.6367 (m-80) cc_final: 0.6122 (m-80) REVERT: a 436 LYS cc_start: 0.7818 (mttt) cc_final: 0.7310 (mptt) REVERT: b 16 ASN cc_start: 0.8734 (m110) cc_final: 0.8529 (m-40) REVERT: b 44 ASP cc_start: 0.6518 (t0) cc_final: 0.6316 (p0) REVERT: b 58 ILE cc_start: 0.8991 (pt) cc_final: 0.8764 (pt) REVERT: b 61 LEU cc_start: 0.8896 (mt) cc_final: 0.8591 (mt) REVERT: b 66 ARG cc_start: 0.8722 (mtp85) cc_final: 0.8020 (mtt-85) REVERT: b 122 GLU cc_start: 0.8580 (tp30) cc_final: 0.8297 (tm-30) REVERT: b 141 ASP cc_start: 0.7754 (m-30) cc_final: 0.7199 (p0) REVERT: b 431 ASP cc_start: 0.8605 (p0) cc_final: 0.8371 (p0) REVERT: c 392 TYR cc_start: 0.7741 (m-80) cc_final: 0.7497 (m-80) REVERT: c 541 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8127 (tp40) REVERT: d 66 ARG cc_start: 0.8792 (mtp85) cc_final: 0.8325 (mtt90) REVERT: d 122 GLU cc_start: 0.8816 (tp30) cc_final: 0.8511 (tp30) REVERT: d 189 LYS cc_start: 0.8108 (pptt) cc_final: 0.7862 (pttt) REVERT: d 299 ASP cc_start: 0.8121 (p0) cc_final: 0.7588 (t0) REVERT: d 315 MET cc_start: 0.6657 (tpt) cc_final: 0.5827 (tmm) REVERT: d 372 ASN cc_start: 0.8401 (m-40) cc_final: 0.7966 (t0) REVERT: d 453 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7447 (mttt) REVERT: e 17 ASN cc_start: 0.7588 (m110) cc_final: 0.7341 (m110) REVERT: e 42 LYS cc_start: 0.7952 (tptt) cc_final: 0.7410 (tmmt) REVERT: e 50 ILE cc_start: 0.9006 (mm) cc_final: 0.8658 (mm) REVERT: e 94 GLU cc_start: 0.6526 (mt-10) cc_final: 0.5957 (tm-30) REVERT: e 122 GLU cc_start: 0.8747 (mm-30) cc_final: 0.7283 (tp30) REVERT: e 180 GLU cc_start: 0.8856 (tp30) cc_final: 0.8499 (tp30) REVERT: e 211 ASP cc_start: 0.7690 (m-30) cc_final: 0.7269 (t70) REVERT: e 271 LEU cc_start: 0.7717 (mm) cc_final: 0.7234 (mm) REVERT: e 276 ASN cc_start: 0.6609 (m-40) cc_final: 0.6373 (m-40) REVERT: e 315 MET cc_start: 0.7604 (tpp) cc_final: 0.6592 (mtm) REVERT: e 406 MET cc_start: 0.4018 (mmm) cc_final: 0.3481 (mmp) REVERT: e 468 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8562 (mp) REVERT: e 501 GLU cc_start: 0.8161 (tt0) cc_final: 0.7811 (tp30) REVERT: f 15 GLN cc_start: 0.8205 (mt0) cc_final: 0.7977 (mm110) REVERT: f 114 ASP cc_start: 0.8622 (t70) cc_final: 0.8385 (t0) REVERT: f 122 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8374 (tp30) REVERT: f 207 THR cc_start: 0.7796 (m) cc_final: 0.7369 (p) REVERT: f 209 TYR cc_start: 0.8122 (m-10) cc_final: 0.7626 (m-10) REVERT: f 232 LYS cc_start: 0.7982 (tptp) cc_final: 0.7393 (mttm) REVERT: f 278 GLN cc_start: 0.6204 (mm110) cc_final: 0.5954 (mt0) REVERT: f 314 TYR cc_start: 0.6866 (m-80) cc_final: 0.6090 (m-80) REVERT: f 501 GLU cc_start: 0.8855 (tp30) cc_final: 0.8413 (tp30) REVERT: g 30 GLU cc_start: 0.7491 (tt0) cc_final: 0.7240 (tt0) REVERT: g 87 ASN cc_start: 0.7703 (m110) cc_final: 0.7422 (m110) REVERT: g 144 MET cc_start: 0.8725 (ttt) cc_final: 0.8401 (ttt) REVERT: g 235 THR cc_start: 0.7865 (p) cc_final: 0.7393 (t) REVERT: g 250 TYR cc_start: 0.5934 (m-80) cc_final: 0.5486 (m-80) REVERT: g 367 MET cc_start: 0.5317 (mpp) cc_final: 0.4287 (mtt) REVERT: g 492 LEU cc_start: 0.9313 (tp) cc_final: 0.8943 (tp) REVERT: h 22 GLN cc_start: 0.9037 (tp40) cc_final: 0.8718 (tp40) REVERT: h 232 LYS cc_start: 0.7360 (tttt) cc_final: 0.6922 (tppt) REVERT: h 367 MET cc_start: 0.8751 (mpp) cc_final: 0.8136 (mpp) REVERT: h 408 ASN cc_start: 0.8065 (m110) cc_final: 0.7797 (t0) outliers start: 8 outliers final: 0 residues processed: 1911 average time/residue: 0.7297 time to fit residues: 2499.1261 Evaluate side-chains 1436 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1435 time to evaluate : 7.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1116 optimal weight: 9.9990 chunk 849 optimal weight: 10.0000 chunk 586 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 539 optimal weight: 8.9990 chunk 758 optimal weight: 10.0000 chunk 1133 optimal weight: 20.0000 chunk 1200 optimal weight: 6.9990 chunk 592 optimal weight: 0.9990 chunk 1074 optimal weight: 0.9980 chunk 323 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 3 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 171 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 ASN ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 GLN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN d 349 GLN d 537 GLN e 3 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 ASN ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 91126 Z= 0.187 Angle : 0.563 11.168 123878 Z= 0.304 Chirality : 0.039 0.338 15249 Planarity : 0.003 0.052 16583 Dihedral : 4.631 32.315 13110 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.52 (0.08), residues: 12512 helix: 3.02 (0.07), residues: 5406 sheet: 0.16 (0.14), residues: 1321 loop : -2.47 (0.07), residues: 5785 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE f 374 TYR 0.019 0.001 TYR C 511 ARG 0.006 0.001 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1926 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1919 time to evaluate : 7.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8532 (tt0) cc_final: 0.7931 (tp30) REVERT: A 115 GLU cc_start: 0.8500 (tt0) cc_final: 0.8187 (tt0) REVERT: A 349 GLN cc_start: 0.9028 (pp30) cc_final: 0.8815 (pp30) REVERT: A 358 ASP cc_start: 0.7620 (m-30) cc_final: 0.6522 (p0) REVERT: A 362 PHE cc_start: 0.7841 (m-80) cc_final: 0.7424 (m-80) REVERT: A 394 VAL cc_start: 0.7813 (t) cc_final: 0.7374 (p) REVERT: A 419 TYR cc_start: 0.7894 (m-80) cc_final: 0.7493 (m-10) REVERT: A 436 LYS cc_start: 0.8255 (mttt) cc_final: 0.7803 (mttp) REVERT: A 536 ASN cc_start: 0.8042 (m110) cc_final: 0.7237 (t0) REVERT: B 122 GLU cc_start: 0.8715 (tp30) cc_final: 0.8146 (tp30) REVERT: C 264 ASP cc_start: 0.8803 (t70) cc_final: 0.8598 (t70) REVERT: C 284 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8650 (tmtt) REVERT: C 297 ASN cc_start: 0.8717 (m110) cc_final: 0.7976 (t0) REVERT: C 367 MET cc_start: 0.7730 (mpp) cc_final: 0.7247 (mpp) REVERT: C 505 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7104 (ttt180) REVERT: D 30 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 121 ASP cc_start: 0.8255 (t70) cc_final: 0.7731 (t0) REVERT: D 122 GLU cc_start: 0.8549 (tp30) cc_final: 0.8249 (tp30) REVERT: D 189 LYS cc_start: 0.8942 (tptt) cc_final: 0.8705 (tptp) REVERT: D 284 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8557 (ttpp) REVERT: D 358 ASP cc_start: 0.8299 (m-30) cc_final: 0.7885 (t0) REVERT: D 367 MET cc_start: 0.8876 (pmm) cc_final: 0.8434 (pmm) REVERT: D 370 ASP cc_start: 0.8573 (t0) cc_final: 0.8341 (m-30) REVERT: D 423 ASP cc_start: 0.8358 (p0) cc_final: 0.7749 (t0) REVERT: D 537 GLN cc_start: 0.7999 (tp40) cc_final: 0.7374 (tt0) REVERT: E 5 ILE cc_start: 0.5579 (mm) cc_final: 0.5334 (mm) REVERT: E 144 MET cc_start: 0.8566 (ttt) cc_final: 0.8161 (ttm) REVERT: E 363 ASP cc_start: 0.5828 (m-30) cc_final: 0.5227 (t70) REVERT: E 406 MET cc_start: 0.7578 (mtm) cc_final: 0.7108 (mtt) REVERT: F 44 ASP cc_start: 0.7566 (m-30) cc_final: 0.7068 (p0) REVERT: F 100 SER cc_start: 0.8998 (m) cc_final: 0.8491 (p) REVERT: F 151 ASN cc_start: 0.8629 (m-40) cc_final: 0.8138 (t0) REVERT: F 232 LYS cc_start: 0.8550 (mppt) cc_final: 0.8240 (mppt) REVERT: F 284 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8036 (tmtt) REVERT: F 380 ASN cc_start: 0.8240 (m-40) cc_final: 0.7538 (t0) REVERT: G 144 MET cc_start: 0.8365 (ttt) cc_final: 0.8101 (ttm) REVERT: G 436 LYS cc_start: 0.8405 (mppt) cc_final: 0.7469 (tptm) REVERT: H 131 GLN cc_start: 0.8700 (pp30) cc_final: 0.8396 (pp30) REVERT: H 168 LEU cc_start: 0.9140 (mp) cc_final: 0.8759 (tp) REVERT: H 423 ASP cc_start: 0.8002 (p0) cc_final: 0.7707 (p0) REVERT: I 161 LYS cc_start: 0.8805 (mptt) cc_final: 0.8469 (mtmt) REVERT: I 176 ASN cc_start: 0.8600 (t0) cc_final: 0.8141 (t0) REVERT: I 232 LYS cc_start: 0.7962 (pttp) cc_final: 0.7700 (pttm) REVERT: I 294 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7379 (tm-30) REVERT: I 406 MET cc_start: 0.4128 (mmm) cc_final: 0.3808 (tpt) REVERT: I 419 TYR cc_start: 0.7227 (m-80) cc_final: 0.6972 (m-10) REVERT: I 423 ASP cc_start: 0.7744 (p0) cc_final: 0.7279 (p0) REVERT: J 58 ILE cc_start: 0.8487 (pt) cc_final: 0.8125 (mt) REVERT: J 59 LYS cc_start: 0.7103 (mttm) cc_final: 0.6654 (tmtt) REVERT: J 194 PHE cc_start: 0.7009 (t80) cc_final: 0.6447 (t80) REVERT: J 314 TYR cc_start: 0.6556 (m-80) cc_final: 0.6326 (m-80) REVERT: J 367 MET cc_start: 0.5645 (mpp) cc_final: 0.5018 (mpp) REVERT: J 406 MET cc_start: 0.7516 (mmm) cc_final: 0.7241 (mmm) REVERT: K 114 ASP cc_start: 0.8990 (t0) cc_final: 0.8723 (m-30) REVERT: K 116 ILE cc_start: 0.9377 (mm) cc_final: 0.9026 (tp) REVERT: K 265 ASP cc_start: 0.6940 (p0) cc_final: 0.6588 (m-30) REVERT: K 372 ASN cc_start: 0.8691 (m110) cc_final: 0.8390 (t0) REVERT: K 406 MET cc_start: 0.4784 (tpt) cc_final: 0.3496 (ptm) REVERT: K 410 VAL cc_start: 0.8267 (p) cc_final: 0.7843 (p) REVERT: K 547 GLN cc_start: 0.7192 (pp30) cc_final: 0.6794 (pp30) REVERT: L 19 ASN cc_start: 0.8371 (m-40) cc_final: 0.7775 (t0) REVERT: L 274 PHE cc_start: 0.7493 (t80) cc_final: 0.6499 (t80) REVERT: L 367 MET cc_start: 0.7811 (ppp) cc_final: 0.6477 (tpp) REVERT: L 501 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7787 (mm-30) REVERT: M 19 ASN cc_start: 0.8660 (m-40) cc_final: 0.7859 (t0) REVERT: M 122 GLU cc_start: 0.7999 (tp30) cc_final: 0.6783 (mt-10) REVERT: M 140 LYS cc_start: 0.8493 (ptpt) cc_final: 0.7741 (mttp) REVERT: M 351 ASP cc_start: 0.8725 (p0) cc_final: 0.8419 (t0) REVERT: M 472 ASP cc_start: 0.7616 (m-30) cc_final: 0.7300 (m-30) REVERT: M 482 GLN cc_start: 0.8712 (tt0) cc_final: 0.8306 (tt0) REVERT: M 525 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8322 (tp40) REVERT: N 108 ASP cc_start: 0.8545 (m-30) cc_final: 0.8329 (m-30) REVERT: N 140 LYS cc_start: 0.8377 (mttt) cc_final: 0.8051 (mttp) REVERT: N 173 PHE cc_start: 0.8654 (t80) cc_final: 0.8404 (t80) REVERT: N 180 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7931 (mm-30) REVERT: N 217 SER cc_start: 0.7798 (t) cc_final: 0.7533 (p) REVERT: N 220 ASP cc_start: 0.8726 (m-30) cc_final: 0.8246 (m-30) REVERT: N 405 TYR cc_start: 0.7070 (m-80) cc_final: 0.6595 (m-80) REVERT: O 42 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8306 (ttmt) REVERT: O 66 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7322 (mmt180) REVERT: O 88 ASN cc_start: 0.8835 (m-40) cc_final: 0.8452 (t0) REVERT: O 123 ILE cc_start: 0.8409 (mt) cc_final: 0.7486 (mt) REVERT: O 344 LYS cc_start: 0.6929 (tptm) cc_final: 0.6382 (tptp) REVERT: O 406 MET cc_start: 0.8223 (mmp) cc_final: 0.7823 (mmm) REVERT: O 498 ASN cc_start: 0.7554 (m110) cc_final: 0.7270 (m110) REVERT: a 115 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7977 (tp30) REVERT: a 241 PHE cc_start: 0.7468 (m-80) cc_final: 0.7055 (m-80) REVERT: a 315 MET cc_start: 0.6729 (mmp) cc_final: 0.6409 (tpt) REVERT: a 392 TYR cc_start: 0.6342 (m-80) cc_final: 0.6041 (m-80) REVERT: a 406 MET cc_start: 0.7120 (mmm) cc_final: 0.6375 (mmm) REVERT: a 436 LYS cc_start: 0.7811 (mttt) cc_final: 0.7312 (mptt) REVERT: b 44 ASP cc_start: 0.6504 (t0) cc_final: 0.6243 (p0) REVERT: b 58 ILE cc_start: 0.8975 (pt) cc_final: 0.8765 (pt) REVERT: b 61 LEU cc_start: 0.8920 (mt) cc_final: 0.8661 (mt) REVERT: b 66 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8124 (mtt-85) REVERT: b 141 ASP cc_start: 0.7705 (m-30) cc_final: 0.7152 (p0) REVERT: b 315 MET cc_start: 0.5173 (ppp) cc_final: 0.4683 (ppp) REVERT: b 431 ASP cc_start: 0.8621 (p0) cc_final: 0.8407 (p0) REVERT: b 484 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.5018 (tpt170) REVERT: c 32 LEU cc_start: 0.8259 (tp) cc_final: 0.7882 (tt) REVERT: c 79 GLU cc_start: 0.8358 (tp30) cc_final: 0.8089 (tp30) REVERT: c 131 GLN cc_start: 0.8207 (pp30) cc_final: 0.7938 (pp30) REVERT: c 144 MET cc_start: 0.7959 (ttt) cc_final: 0.7425 (ttt) REVERT: c 392 TYR cc_start: 0.7740 (m-80) cc_final: 0.7490 (m-80) REVERT: c 541 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8043 (tp40) REVERT: d 39 ASN cc_start: 0.7860 (m-40) cc_final: 0.7600 (m-40) REVERT: d 66 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8335 (mtt90) REVERT: d 122 GLU cc_start: 0.8797 (tp30) cc_final: 0.8472 (tp30) REVERT: d 189 LYS cc_start: 0.8026 (pptt) cc_final: 0.7798 (pttt) REVERT: d 299 ASP cc_start: 0.8101 (p0) cc_final: 0.7554 (t0) REVERT: d 315 MET cc_start: 0.6576 (tpt) cc_final: 0.5782 (tmm) REVERT: d 372 ASN cc_start: 0.8406 (m-40) cc_final: 0.7819 (t0) REVERT: d 453 LYS cc_start: 0.7899 (tmmt) cc_final: 0.7429 (mttt) REVERT: e 17 ASN cc_start: 0.7590 (m110) cc_final: 0.7341 (m110) REVERT: e 30 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8334 (tm-30) REVERT: e 42 LYS cc_start: 0.7942 (tptt) cc_final: 0.7450 (tmmt) REVERT: e 50 ILE cc_start: 0.8917 (mm) cc_final: 0.8601 (mm) REVERT: e 94 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5994 (tm-30) REVERT: e 122 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7286 (tp30) REVERT: e 211 ASP cc_start: 0.7604 (m-30) cc_final: 0.7149 (t70) REVERT: e 271 LEU cc_start: 0.7772 (mm) cc_final: 0.7393 (mm) REVERT: e 276 ASN cc_start: 0.6529 (m-40) cc_final: 0.6300 (m-40) REVERT: e 406 MET cc_start: 0.4109 (mmm) cc_final: 0.3613 (mmp) REVERT: e 468 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8523 (mp) REVERT: e 501 GLU cc_start: 0.8133 (tt0) cc_final: 0.7806 (tp30) REVERT: e 514 GLU cc_start: 0.7961 (tp30) cc_final: 0.7711 (tp30) REVERT: f 15 GLN cc_start: 0.8292 (mt0) cc_final: 0.8027 (mm110) REVERT: f 76 GLN cc_start: 0.8695 (mt0) cc_final: 0.8447 (mt0) REVERT: f 114 ASP cc_start: 0.8528 (t70) cc_final: 0.8323 (t0) REVERT: f 122 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8363 (tp30) REVERT: f 232 LYS cc_start: 0.7873 (tptp) cc_final: 0.7387 (mttm) REVERT: f 278 GLN cc_start: 0.6206 (mm110) cc_final: 0.5945 (mt0) REVERT: f 501 GLU cc_start: 0.8746 (tp30) cc_final: 0.8344 (tp30) REVERT: g 17 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7856 (t0) REVERT: g 30 GLU cc_start: 0.7404 (tt0) cc_final: 0.7198 (tt0) REVERT: g 87 ASN cc_start: 0.7976 (m110) cc_final: 0.7560 (m110) REVERT: g 141 ASP cc_start: 0.8310 (t0) cc_final: 0.8006 (t0) REVERT: g 144 MET cc_start: 0.8731 (ttt) cc_final: 0.8473 (ttt) REVERT: g 250 TYR cc_start: 0.5860 (m-80) cc_final: 0.5426 (m-80) REVERT: g 367 MET cc_start: 0.5605 (mpp) cc_final: 0.4764 (mtt) REVERT: h 22 GLN cc_start: 0.8995 (tp40) cc_final: 0.8300 (tp40) REVERT: h 38 ILE cc_start: 0.9334 (mm) cc_final: 0.9043 (mm) REVERT: h 232 LYS cc_start: 0.7062 (tttp) cc_final: 0.6767 (tppt) REVERT: h 367 MET cc_start: 0.8761 (mpp) cc_final: 0.8245 (mpp) REVERT: h 408 ASN cc_start: 0.8120 (m110) cc_final: 0.7620 (t0) REVERT: h 445 LYS cc_start: 0.8635 (mppt) cc_final: 0.7771 (tttt) outliers start: 7 outliers final: 1 residues processed: 1925 average time/residue: 0.7306 time to fit residues: 2507.0945 Evaluate side-chains 1466 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1463 time to evaluate : 7.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 999 optimal weight: 8.9990 chunk 681 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 893 optimal weight: 9.9990 chunk 495 optimal weight: 9.9990 chunk 1024 optimal weight: 2.9990 chunk 829 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 613 optimal weight: 9.9990 chunk 1077 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 17 ASN A 63 GLN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 536 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 349 GLN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN F 6 ASN F 86 ASN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 52 ASN H 331 GLN H 376 ASN H 498 ASN H 529 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 ASN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 ASN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 136 ASN ** M 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN a 90 GLN a 113 GLN a 171 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 98 GLN ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 63 GLN ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 ASN d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 297 ASN ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 113 GLN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 320 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 526 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 91126 Z= 0.374 Angle : 0.702 13.115 123878 Z= 0.382 Chirality : 0.043 0.402 15249 Planarity : 0.004 0.053 16583 Dihedral : 5.334 38.783 13110 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.04 % Favored : 89.88 % Rotamer: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.02 (0.08), residues: 12512 helix: 2.52 (0.07), residues: 5325 sheet: -0.33 (0.13), residues: 1464 loop : -2.61 (0.07), residues: 5723 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE h 173 TYR 0.024 0.002 TYR f 259 ARG 0.012 0.001 ARG O 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1769 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1762 time to evaluate : 7.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8676 (tt0) cc_final: 0.7986 (tp30) REVERT: A 95 LEU cc_start: 0.9292 (mt) cc_final: 0.9003 (mt) REVERT: A 115 GLU cc_start: 0.8580 (tt0) cc_final: 0.8304 (tt0) REVERT: A 171 ASN cc_start: 0.7851 (t0) cc_final: 0.7539 (t0) REVERT: A 315 MET cc_start: 0.8085 (mmm) cc_final: 0.7758 (mmm) REVERT: A 349 GLN cc_start: 0.9122 (pp30) cc_final: 0.8829 (pp30) REVERT: A 358 ASP cc_start: 0.7648 (m-30) cc_final: 0.6500 (p0) REVERT: A 394 VAL cc_start: 0.8277 (t) cc_final: 0.7881 (p) REVERT: B 122 GLU cc_start: 0.8754 (tp30) cc_final: 0.8116 (tp30) REVERT: B 129 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7877 (mm-40) REVERT: B 264 ASP cc_start: 0.7658 (t0) cc_final: 0.7416 (t0) REVERT: B 362 PHE cc_start: 0.4032 (m-80) cc_final: 0.3511 (m-80) REVERT: B 405 TYR cc_start: 0.5579 (m-80) cc_final: 0.5251 (m-10) REVERT: B 426 ILE cc_start: 0.9273 (mm) cc_final: 0.9050 (mm) REVERT: B 518 MET cc_start: 0.8260 (tpt) cc_final: 0.7932 (tpt) REVERT: C 30 GLU cc_start: 0.7435 (tt0) cc_final: 0.6963 (tp30) REVERT: C 264 ASP cc_start: 0.8863 (t70) cc_final: 0.8655 (t0) REVERT: C 276 ASN cc_start: 0.8697 (m-40) cc_final: 0.7976 (m-40) REVERT: C 284 LYS cc_start: 0.9278 (mmmt) cc_final: 0.8772 (tmtt) REVERT: C 297 ASN cc_start: 0.8680 (m110) cc_final: 0.8005 (t0) REVERT: C 505 ARG cc_start: 0.8208 (ttm110) cc_final: 0.6984 (ttt180) REVERT: D 30 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 121 ASP cc_start: 0.8234 (t70) cc_final: 0.7696 (t0) REVERT: D 122 GLU cc_start: 0.8746 (tp30) cc_final: 0.8459 (tp30) REVERT: D 154 GLN cc_start: 0.7420 (mt0) cc_final: 0.7059 (mt0) REVERT: D 284 LYS cc_start: 0.8995 (mmtm) cc_final: 0.8636 (ttpp) REVERT: D 423 ASP cc_start: 0.8494 (p0) cc_final: 0.7808 (t0) REVERT: D 537 GLN cc_start: 0.8204 (tp40) cc_final: 0.7489 (tt0) REVERT: E 61 LEU cc_start: 0.9073 (mt) cc_final: 0.8844 (mt) REVERT: E 144 MET cc_start: 0.8883 (ttt) cc_final: 0.8439 (ttm) REVERT: E 363 ASP cc_start: 0.5895 (m-30) cc_final: 0.5208 (t70) REVERT: E 406 MET cc_start: 0.7749 (mtm) cc_final: 0.7199 (mtp) REVERT: F 44 ASP cc_start: 0.7736 (m-30) cc_final: 0.7290 (p0) REVERT: F 151 ASN cc_start: 0.8647 (m-40) cc_final: 0.8198 (t0) REVERT: F 232 LYS cc_start: 0.8642 (mppt) cc_final: 0.8238 (mppt) REVERT: F 284 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8194 (tmtt) REVERT: F 380 ASN cc_start: 0.8374 (m-40) cc_final: 0.7906 (t0) REVERT: F 537 GLN cc_start: 0.8145 (pp30) cc_final: 0.7911 (pp30) REVERT: G 144 MET cc_start: 0.8377 (ttt) cc_final: 0.8066 (ttm) REVERT: H 38 ILE cc_start: 0.8468 (mp) cc_final: 0.8057 (mt) REVERT: H 131 GLN cc_start: 0.8754 (pp30) cc_final: 0.8409 (pp30) REVERT: H 168 LEU cc_start: 0.9129 (mp) cc_final: 0.8820 (tp) REVERT: H 376 ASN cc_start: 0.8618 (m-40) cc_final: 0.8387 (m110) REVERT: H 423 ASP cc_start: 0.8142 (p0) cc_final: 0.7796 (p0) REVERT: H 465 ASP cc_start: 0.9295 (m-30) cc_final: 0.9033 (m-30) REVERT: I 94 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8374 (tm-30) REVERT: I 108 ASP cc_start: 0.8624 (m-30) cc_final: 0.8373 (m-30) REVERT: I 161 LYS cc_start: 0.8931 (mptt) cc_final: 0.8452 (mtmt) REVERT: I 294 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7395 (tm-30) REVERT: I 406 MET cc_start: 0.4213 (mmm) cc_final: 0.3705 (tpt) REVERT: I 419 TYR cc_start: 0.7425 (m-80) cc_final: 0.7143 (m-10) REVERT: I 423 ASP cc_start: 0.7552 (p0) cc_final: 0.7055 (p0) REVERT: J 58 ILE cc_start: 0.8516 (pt) cc_final: 0.8197 (mt) REVERT: J 59 LYS cc_start: 0.7134 (mttm) cc_final: 0.6663 (tmtt) REVERT: J 122 GLU cc_start: 0.8881 (tp30) cc_final: 0.8575 (tp30) REVERT: J 250 TYR cc_start: 0.4257 (m-10) cc_final: 0.3756 (m-10) REVERT: J 314 TYR cc_start: 0.6736 (m-80) cc_final: 0.6439 (m-80) REVERT: J 406 MET cc_start: 0.7586 (mmm) cc_final: 0.7366 (mmm) REVERT: K 42 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8681 (tppt) REVERT: K 114 ASP cc_start: 0.9022 (t0) cc_final: 0.8807 (m-30) REVERT: K 372 ASN cc_start: 0.8651 (m110) cc_final: 0.8322 (t0) REVERT: K 406 MET cc_start: 0.4914 (tpt) cc_final: 0.3625 (ptm) REVERT: K 410 VAL cc_start: 0.8275 (p) cc_final: 0.7744 (p) REVERT: K 547 GLN cc_start: 0.7609 (pp30) cc_final: 0.7257 (pp30) REVERT: L 19 ASN cc_start: 0.8607 (m-40) cc_final: 0.7982 (t0) REVERT: L 129 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7496 (mm-40) REVERT: L 274 PHE cc_start: 0.7503 (t80) cc_final: 0.6637 (t80) REVERT: L 367 MET cc_start: 0.7952 (ppp) cc_final: 0.6580 (tpp) REVERT: L 501 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7625 (mm-30) REVERT: M 19 ASN cc_start: 0.8771 (m-40) cc_final: 0.8023 (t0) REVERT: M 122 GLU cc_start: 0.8207 (tp30) cc_final: 0.6831 (mt-10) REVERT: M 140 LYS cc_start: 0.8440 (ptpt) cc_final: 0.7887 (mttp) REVERT: M 176 ASN cc_start: 0.8032 (p0) cc_final: 0.7809 (p0) REVERT: M 241 PHE cc_start: 0.6736 (m-80) cc_final: 0.6424 (m-80) REVERT: M 525 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8470 (tp40) REVERT: N 108 ASP cc_start: 0.8575 (m-30) cc_final: 0.8247 (m-30) REVERT: N 114 ASP cc_start: 0.7994 (m-30) cc_final: 0.7759 (m-30) REVERT: O 88 ASN cc_start: 0.8941 (m-40) cc_final: 0.8475 (t0) REVERT: O 123 ILE cc_start: 0.8496 (mt) cc_final: 0.7821 (mt) REVERT: O 173 PHE cc_start: 0.8731 (t80) cc_final: 0.8373 (t80) REVERT: O 314 TYR cc_start: 0.8668 (m-10) cc_final: 0.8399 (m-10) REVERT: O 498 ASN cc_start: 0.7671 (m110) cc_final: 0.7334 (m110) REVERT: a 79 GLU cc_start: 0.8304 (tp30) cc_final: 0.8038 (tp30) REVERT: a 115 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8178 (tp30) REVERT: a 234 THR cc_start: 0.4919 (p) cc_final: 0.4281 (p) REVERT: a 241 PHE cc_start: 0.7612 (m-80) cc_final: 0.7352 (m-80) REVERT: a 252 TYR cc_start: 0.7110 (m-80) cc_final: 0.6806 (m-80) REVERT: a 314 TYR cc_start: 0.6542 (m-10) cc_final: 0.6169 (m-10) REVERT: a 315 MET cc_start: 0.6667 (mmp) cc_final: 0.6364 (tpt) REVERT: a 362 PHE cc_start: 0.8306 (m-80) cc_final: 0.8053 (m-80) REVERT: a 436 LYS cc_start: 0.7684 (mttt) cc_final: 0.7280 (mptt) REVERT: b 58 ILE cc_start: 0.8997 (pt) cc_final: 0.8752 (pt) REVERT: b 61 LEU cc_start: 0.8899 (mt) cc_final: 0.8602 (mt) REVERT: b 141 ASP cc_start: 0.7796 (m-30) cc_final: 0.7060 (p0) REVERT: b 423 ASP cc_start: 0.8202 (p0) cc_final: 0.7634 (p0) REVERT: b 431 ASP cc_start: 0.8571 (p0) cc_final: 0.8344 (p0) REVERT: c 79 GLU cc_start: 0.8319 (tp30) cc_final: 0.8010 (tp30) REVERT: c 144 MET cc_start: 0.8093 (ttt) cc_final: 0.7709 (ttt) REVERT: c 392 TYR cc_start: 0.7631 (m-80) cc_final: 0.7258 (m-80) REVERT: c 478 LEU cc_start: 0.8943 (pp) cc_final: 0.8573 (pp) REVERT: c 541 GLN cc_start: 0.8881 (mm-40) cc_final: 0.7988 (tp40) REVERT: d 39 ASN cc_start: 0.8012 (m-40) cc_final: 0.7492 (m110) REVERT: d 66 ARG cc_start: 0.8901 (mtp85) cc_final: 0.8560 (mtp85) REVERT: d 122 GLU cc_start: 0.8934 (tp30) cc_final: 0.8357 (tp30) REVERT: d 255 ASP cc_start: 0.7379 (p0) cc_final: 0.6553 (t0) REVERT: d 315 MET cc_start: 0.6890 (tpt) cc_final: 0.6636 (tmm) REVERT: d 367 MET cc_start: 0.6547 (tpp) cc_final: 0.6311 (tpp) REVERT: d 372 ASN cc_start: 0.8743 (m-40) cc_final: 0.8131 (t0) REVERT: d 453 LYS cc_start: 0.8051 (tmmt) cc_final: 0.7578 (mttt) REVERT: d 537 GLN cc_start: 0.8124 (tp40) cc_final: 0.7923 (tp40) REVERT: e 13 ILE cc_start: 0.8562 (mm) cc_final: 0.8190 (mm) REVERT: e 17 ASN cc_start: 0.7613 (m110) cc_final: 0.7365 (m110) REVERT: e 30 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8286 (tm-30) REVERT: e 94 GLU cc_start: 0.6616 (mt-10) cc_final: 0.5907 (tp30) REVERT: e 211 ASP cc_start: 0.7573 (m-30) cc_final: 0.7199 (t70) REVERT: e 271 LEU cc_start: 0.7856 (mm) cc_final: 0.7537 (mm) REVERT: e 406 MET cc_start: 0.4069 (mmm) cc_final: 0.3560 (mmp) REVERT: e 501 GLU cc_start: 0.8208 (tt0) cc_final: 0.7958 (tp30) REVERT: e 514 GLU cc_start: 0.8151 (tp30) cc_final: 0.7858 (tp30) REVERT: f 15 GLN cc_start: 0.8344 (mt0) cc_final: 0.8123 (mm110) REVERT: f 122 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8648 (tp30) REVERT: f 232 LYS cc_start: 0.8223 (tptp) cc_final: 0.7823 (mttm) REVERT: f 314 TYR cc_start: 0.6904 (m-80) cc_final: 0.6590 (m-80) REVERT: f 459 ASP cc_start: 0.7646 (m-30) cc_final: 0.7412 (m-30) REVERT: g 30 GLU cc_start: 0.7670 (tt0) cc_final: 0.7398 (tm-30) REVERT: g 141 ASP cc_start: 0.8348 (t0) cc_final: 0.8089 (t0) REVERT: g 367 MET cc_start: 0.5969 (mpp) cc_final: 0.4723 (mtt) REVERT: g 392 TYR cc_start: 0.7801 (m-10) cc_final: 0.7458 (m-10) REVERT: h 31 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7967 (ttp-170) REVERT: h 232 LYS cc_start: 0.7152 (tttp) cc_final: 0.6825 (tppt) REVERT: h 315 MET cc_start: 0.4932 (tpp) cc_final: 0.4643 (tpp) REVERT: h 367 MET cc_start: 0.8631 (mpp) cc_final: 0.8279 (mpp) REVERT: h 405 TYR cc_start: 0.6313 (m-80) cc_final: 0.5927 (m-10) REVERT: h 445 LYS cc_start: 0.8922 (mppt) cc_final: 0.8025 (tptt) REVERT: h 501 GLU cc_start: 0.8438 (tt0) cc_final: 0.7661 (tt0) outliers start: 7 outliers final: 3 residues processed: 1768 average time/residue: 0.7290 time to fit residues: 2301.9189 Evaluate side-chains 1350 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1347 time to evaluate : 7.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 403 optimal weight: 7.9990 chunk 1081 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 704 optimal weight: 9.9990 chunk 296 optimal weight: 30.0000 chunk 1201 optimal weight: 8.9990 chunk 997 optimal weight: 9.9990 chunk 556 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 397 optimal weight: 6.9990 chunk 630 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 17 ASN A 63 GLN A 67 ASN A 86 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 522 GLN B 541 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 GLN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 ASN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** G 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 52 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 529 ASN K 21 ASN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN L 88 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 ASN ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 21 ASN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 3 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 GLN ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN ** f 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 ASN ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 91126 Z= 0.268 Angle : 0.629 11.028 123878 Z= 0.341 Chirality : 0.041 0.357 15249 Planarity : 0.003 0.052 16583 Dihedral : 5.149 36.396 13110 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.46 % Favored : 90.52 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.08 (0.08), residues: 12512 helix: 2.72 (0.07), residues: 5328 sheet: -0.40 (0.13), residues: 1387 loop : -2.61 (0.07), residues: 5797 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE F 173 TYR 0.017 0.002 TYR C 511 ARG 0.012 0.001 ARG L 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1763 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1757 time to evaluate : 7.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8603 (tt0) cc_final: 0.7916 (tp30) REVERT: A 95 LEU cc_start: 0.9262 (mt) cc_final: 0.8939 (mt) REVERT: A 115 GLU cc_start: 0.8532 (tt0) cc_final: 0.8288 (tt0) REVERT: A 171 ASN cc_start: 0.8073 (t0) cc_final: 0.7819 (t0) REVERT: A 315 MET cc_start: 0.8048 (mmm) cc_final: 0.7728 (mmm) REVERT: A 349 GLN cc_start: 0.8965 (pp30) cc_final: 0.8738 (pp30) REVERT: A 406 MET cc_start: 0.7576 (tpt) cc_final: 0.7218 (tpt) REVERT: A 436 LYS cc_start: 0.8259 (mttt) cc_final: 0.7824 (mttp) REVERT: B 122 GLU cc_start: 0.8368 (tp30) cc_final: 0.7625 (tp30) REVERT: B 129 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7810 (mm110) REVERT: B 264 ASP cc_start: 0.7807 (t0) cc_final: 0.7509 (t0) REVERT: B 313 LEU cc_start: 0.8722 (mt) cc_final: 0.8284 (mt) REVERT: B 362 PHE cc_start: 0.3484 (m-80) cc_final: 0.3207 (m-80) REVERT: B 405 TYR cc_start: 0.5731 (m-80) cc_final: 0.5390 (m-10) REVERT: C 30 GLU cc_start: 0.7372 (tt0) cc_final: 0.6924 (tp30) REVERT: C 264 ASP cc_start: 0.8820 (t70) cc_final: 0.8584 (t0) REVERT: C 276 ASN cc_start: 0.8644 (m-40) cc_final: 0.8290 (m-40) REVERT: C 284 LYS cc_start: 0.9324 (mmmt) cc_final: 0.8798 (tmtt) REVERT: C 297 ASN cc_start: 0.8515 (m110) cc_final: 0.8004 (t0) REVERT: C 501 GLU cc_start: 0.8486 (tp30) cc_final: 0.7825 (tm-30) REVERT: C 505 ARG cc_start: 0.8109 (ttm110) cc_final: 0.6815 (ttt180) REVERT: D 30 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6455 (tm-30) REVERT: D 121 ASP cc_start: 0.8263 (t70) cc_final: 0.7708 (t0) REVERT: D 122 GLU cc_start: 0.8690 (tp30) cc_final: 0.8440 (tp30) REVERT: D 284 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8639 (ttpp) REVERT: D 367 MET cc_start: 0.8960 (pmm) cc_final: 0.8509 (pmm) REVERT: D 423 ASP cc_start: 0.8466 (p0) cc_final: 0.7862 (t0) REVERT: D 469 SER cc_start: 0.8751 (t) cc_final: 0.8550 (t) REVERT: D 537 GLN cc_start: 0.8137 (tp40) cc_final: 0.7450 (tt0) REVERT: E 363 ASP cc_start: 0.5719 (m-30) cc_final: 0.4908 (t70) REVERT: E 384 THR cc_start: 0.8371 (p) cc_final: 0.8150 (t) REVERT: E 406 MET cc_start: 0.7695 (mtm) cc_final: 0.7023 (mtp) REVERT: F 44 ASP cc_start: 0.7726 (m-30) cc_final: 0.7248 (p0) REVERT: F 151 ASN cc_start: 0.8616 (m-40) cc_final: 0.8203 (t0) REVERT: F 232 LYS cc_start: 0.8668 (mppt) cc_final: 0.8266 (mppt) REVERT: F 284 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8144 (tmtt) REVERT: F 380 ASN cc_start: 0.8399 (m-40) cc_final: 0.8006 (t0) REVERT: F 537 GLN cc_start: 0.8155 (pp30) cc_final: 0.7885 (pp30) REVERT: G 161 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8623 (mtpt) REVERT: H 38 ILE cc_start: 0.8432 (mp) cc_final: 0.8049 (mt) REVERT: H 131 GLN cc_start: 0.8741 (pp30) cc_final: 0.8434 (pp30) REVERT: H 168 LEU cc_start: 0.9221 (mp) cc_final: 0.8856 (tp) REVERT: H 423 ASP cc_start: 0.8228 (p0) cc_final: 0.7910 (p0) REVERT: H 465 ASP cc_start: 0.9270 (m-30) cc_final: 0.9041 (m-30) REVERT: I 94 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8323 (tm-30) REVERT: I 108 ASP cc_start: 0.8529 (m-30) cc_final: 0.8295 (m-30) REVERT: I 161 LYS cc_start: 0.8872 (mptt) cc_final: 0.8369 (mtmt) REVERT: I 294 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7359 (tm-30) REVERT: I 406 MET cc_start: 0.4065 (mmm) cc_final: 0.3621 (tpt) REVERT: I 419 TYR cc_start: 0.7387 (m-80) cc_final: 0.7163 (m-10) REVERT: I 423 ASP cc_start: 0.7742 (p0) cc_final: 0.6630 (t0) REVERT: I 427 THR cc_start: 0.6587 (p) cc_final: 0.6382 (p) REVERT: J 58 ILE cc_start: 0.8493 (pt) cc_final: 0.8173 (mt) REVERT: J 59 LYS cc_start: 0.7104 (mttm) cc_final: 0.6645 (tmtt) REVERT: J 314 TYR cc_start: 0.6716 (m-80) cc_final: 0.6384 (m-80) REVERT: J 406 MET cc_start: 0.7664 (mmm) cc_final: 0.7432 (mmm) REVERT: J 529 ASN cc_start: 0.8865 (m-40) cc_final: 0.8595 (m110) REVERT: K 114 ASP cc_start: 0.9042 (t0) cc_final: 0.8817 (m-30) REVERT: K 372 ASN cc_start: 0.8624 (m110) cc_final: 0.8301 (t0) REVERT: K 406 MET cc_start: 0.5025 (tpt) cc_final: 0.3769 (ptm) REVERT: K 410 VAL cc_start: 0.8239 (p) cc_final: 0.7653 (p) REVERT: K 547 GLN cc_start: 0.7722 (pp30) cc_final: 0.7359 (pp30) REVERT: L 19 ASN cc_start: 0.8540 (m-40) cc_final: 0.7879 (t0) REVERT: L 129 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7422 (mm-40) REVERT: L 518 MET cc_start: 0.8901 (ttp) cc_final: 0.8517 (ttp) REVERT: M 115 GLU cc_start: 0.8387 (tt0) cc_final: 0.8184 (tt0) REVERT: M 122 GLU cc_start: 0.8187 (tp30) cc_final: 0.6761 (mt-10) REVERT: M 140 LYS cc_start: 0.8448 (ptpt) cc_final: 0.7924 (mttp) REVERT: M 154 GLN cc_start: 0.7469 (mp-120) cc_final: 0.7154 (mp10) REVERT: M 472 ASP cc_start: 0.7669 (m-30) cc_final: 0.7443 (m-30) REVERT: M 482 GLN cc_start: 0.8776 (tt0) cc_final: 0.8543 (tt0) REVERT: M 511 TYR cc_start: 0.8122 (m-80) cc_final: 0.7849 (m-80) REVERT: M 525 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8393 (tp40) REVERT: M 537 GLN cc_start: 0.8636 (mp10) cc_final: 0.8351 (mp10) REVERT: N 108 ASP cc_start: 0.8306 (m-30) cc_final: 0.7961 (m-30) REVERT: N 114 ASP cc_start: 0.7995 (m-30) cc_final: 0.7730 (m-30) REVERT: N 315 MET cc_start: 0.6825 (ppp) cc_final: 0.6319 (mtt) REVERT: N 405 TYR cc_start: 0.7471 (m-80) cc_final: 0.7264 (m-80) REVERT: O 66 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.7344 (mmt180) REVERT: O 88 ASN cc_start: 0.8911 (m-40) cc_final: 0.8366 (t0) REVERT: O 123 ILE cc_start: 0.8484 (mt) cc_final: 0.7864 (mt) REVERT: O 173 PHE cc_start: 0.8482 (t80) cc_final: 0.8231 (t80) REVERT: O 344 LYS cc_start: 0.7255 (tptm) cc_final: 0.7011 (tptp) REVERT: O 390 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8073 (mmtt) REVERT: O 406 MET cc_start: 0.8212 (mmp) cc_final: 0.7991 (mmm) REVERT: a 43 ASP cc_start: 0.5737 (m-30) cc_final: 0.5514 (m-30) REVERT: a 79 GLU cc_start: 0.8299 (tp30) cc_final: 0.7986 (tp30) REVERT: a 115 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8203 (tp30) REVERT: a 234 THR cc_start: 0.4977 (p) cc_final: 0.4371 (p) REVERT: a 241 PHE cc_start: 0.7607 (m-80) cc_final: 0.7362 (m-80) REVERT: a 252 TYR cc_start: 0.7051 (m-80) cc_final: 0.6834 (m-80) REVERT: a 315 MET cc_start: 0.6624 (mmp) cc_final: 0.6065 (tpp) REVERT: a 436 LYS cc_start: 0.7749 (mttt) cc_final: 0.7294 (mptt) REVERT: b 58 ILE cc_start: 0.8954 (pt) cc_final: 0.8746 (pt) REVERT: b 61 LEU cc_start: 0.8967 (mt) cc_final: 0.8696 (mt) REVERT: b 95 LEU cc_start: 0.8831 (mt) cc_final: 0.8507 (mt) REVERT: b 141 ASP cc_start: 0.7816 (m-30) cc_final: 0.7059 (p0) REVERT: b 423 ASP cc_start: 0.8267 (p0) cc_final: 0.7788 (p0) REVERT: c 79 GLU cc_start: 0.8330 (tp30) cc_final: 0.7973 (tp30) REVERT: c 144 MET cc_start: 0.8048 (ttt) cc_final: 0.7743 (ttt) REVERT: c 225 VAL cc_start: 0.8921 (m) cc_final: 0.8667 (p) REVERT: c 392 TYR cc_start: 0.7600 (m-80) cc_final: 0.7261 (m-80) REVERT: c 478 LEU cc_start: 0.8898 (pp) cc_final: 0.8446 (pp) REVERT: d 21 ASN cc_start: 0.8010 (t0) cc_final: 0.7669 (t0) REVERT: d 39 ASN cc_start: 0.8030 (m-40) cc_final: 0.7366 (m110) REVERT: d 66 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8608 (mtp85) REVERT: d 122 GLU cc_start: 0.9033 (tp30) cc_final: 0.8401 (tp30) REVERT: d 189 LYS cc_start: 0.8064 (pptt) cc_final: 0.7820 (pttt) REVERT: d 255 ASP cc_start: 0.7310 (p0) cc_final: 0.6412 (t0) REVERT: d 280 ARG cc_start: 0.7219 (ptp-110) cc_final: 0.6996 (ptm160) REVERT: d 367 MET cc_start: 0.6491 (tpp) cc_final: 0.6278 (tpp) REVERT: d 501 GLU cc_start: 0.8070 (tt0) cc_final: 0.7662 (mm-30) REVERT: e 13 ILE cc_start: 0.8541 (mm) cc_final: 0.8131 (mm) REVERT: e 17 ASN cc_start: 0.7667 (m110) cc_final: 0.7400 (m110) REVERT: e 30 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8259 (tm-30) REVERT: e 94 GLU cc_start: 0.6599 (mt-10) cc_final: 0.5935 (tp30) REVERT: e 211 ASP cc_start: 0.7519 (m-30) cc_final: 0.7114 (t70) REVERT: e 271 LEU cc_start: 0.7938 (mm) cc_final: 0.7704 (mm) REVERT: e 315 MET cc_start: 0.7419 (tpp) cc_final: 0.6540 (mtm) REVERT: e 406 MET cc_start: 0.3976 (mmm) cc_final: 0.3351 (mmt) REVERT: e 501 GLU cc_start: 0.8154 (tt0) cc_final: 0.7947 (tp30) REVERT: e 514 GLU cc_start: 0.8043 (tp30) cc_final: 0.7769 (tp30) REVERT: e 518 MET cc_start: 0.9120 (tmm) cc_final: 0.8710 (tmm) REVERT: f 15 GLN cc_start: 0.8327 (mt0) cc_final: 0.8120 (mm110) REVERT: f 195 THR cc_start: 0.7990 (t) cc_final: 0.7725 (m) REVERT: f 232 LYS cc_start: 0.8138 (tptp) cc_final: 0.7800 (mttm) REVERT: f 314 TYR cc_start: 0.6884 (m-80) cc_final: 0.6653 (m-80) REVERT: f 459 ASP cc_start: 0.7671 (m-30) cc_final: 0.7373 (m-30) REVERT: f 501 GLU cc_start: 0.8539 (tp30) cc_final: 0.8229 (tp30) REVERT: g 141 ASP cc_start: 0.8447 (t0) cc_final: 0.8171 (t0) REVERT: g 278 GLN cc_start: 0.8139 (mp10) cc_final: 0.7425 (pt0) REVERT: g 367 MET cc_start: 0.5948 (mpp) cc_final: 0.4765 (mtt) REVERT: h 22 GLN cc_start: 0.9078 (tp40) cc_final: 0.8636 (tp40) REVERT: h 31 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8066 (ttp-170) REVERT: h 232 LYS cc_start: 0.7224 (tttp) cc_final: 0.6886 (tppt) REVERT: h 313 LEU cc_start: 0.7619 (mt) cc_final: 0.7391 (mt) REVERT: h 315 MET cc_start: 0.5230 (tpp) cc_final: 0.5015 (tpp) REVERT: h 367 MET cc_start: 0.8710 (mpp) cc_final: 0.8350 (mpp) REVERT: h 445 LYS cc_start: 0.8947 (mppt) cc_final: 0.8043 (tptm) outliers start: 6 outliers final: 1 residues processed: 1762 average time/residue: 0.7365 time to fit residues: 2324.9090 Evaluate side-chains 1358 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1357 time to evaluate : 7.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1158 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 684 optimal weight: 30.0000 chunk 877 optimal weight: 0.4980 chunk 679 optimal weight: 20.0000 chunk 1011 optimal weight: 10.0000 chunk 671 optimal weight: 10.0000 chunk 1197 optimal weight: 0.9980 chunk 749 optimal weight: 0.9990 chunk 729 optimal weight: 2.9990 chunk 552 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 63 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN B 63 GLN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 52 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 ASN H 529 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN N 276 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN O 303 ASN ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 270 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 537 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 91126 Z= 0.203 Angle : 0.592 11.200 123878 Z= 0.319 Chirality : 0.040 0.399 15249 Planarity : 0.003 0.049 16583 Dihedral : 4.904 33.820 13110 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.28 % 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: 0.26 (0.08), residues: 12512 helix: 2.94 (0.07), residues: 5340 sheet: -0.32 (0.14), residues: 1327 loop : -2.59 (0.07), residues: 5845 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE F 374 TYR 0.018 0.001 TYR C 392 ARG 0.007 0.001 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1792 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1790 time to evaluate : 7.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8555 (tt0) cc_final: 0.7866 (tp30) REVERT: A 95 LEU cc_start: 0.9216 (mt) cc_final: 0.8913 (mt) REVERT: A 115 GLU cc_start: 0.8522 (tt0) cc_final: 0.8288 (tt0) REVERT: A 358 ASP cc_start: 0.7660 (m-30) cc_final: 0.6524 (p0) REVERT: A 406 MET cc_start: 0.7530 (tpt) cc_final: 0.7224 (tpt) REVERT: A 419 TYR cc_start: 0.7865 (m-80) cc_final: 0.7589 (m-10) REVERT: A 436 LYS cc_start: 0.8240 (mttt) cc_final: 0.7789 (mttp) REVERT: B 122 GLU cc_start: 0.8328 (tp30) cc_final: 0.7663 (tp30) REVERT: B 129 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7723 (mm-40) REVERT: B 264 ASP cc_start: 0.7893 (t0) cc_final: 0.7568 (t0) REVERT: B 313 LEU cc_start: 0.8811 (mt) cc_final: 0.8452 (mt) REVERT: B 362 PHE cc_start: 0.3651 (m-80) cc_final: 0.3387 (m-80) REVERT: B 518 MET cc_start: 0.8262 (tpt) cc_final: 0.7911 (tpt) REVERT: C 122 GLU cc_start: 0.8335 (tp30) cc_final: 0.7953 (tt0) REVERT: C 264 ASP cc_start: 0.8778 (t70) cc_final: 0.8549 (t0) REVERT: C 276 ASN cc_start: 0.8706 (m-40) cc_final: 0.7946 (m-40) REVERT: C 284 LYS cc_start: 0.9296 (mmmt) cc_final: 0.8676 (tmtt) REVERT: C 297 ASN cc_start: 0.8501 (m110) cc_final: 0.8002 (t0) REVERT: C 505 ARG cc_start: 0.8093 (ttm110) cc_final: 0.6940 (ttt180) REVERT: D 30 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6306 (tm-30) REVERT: D 39 ASN cc_start: 0.6026 (m110) cc_final: 0.5379 (m-40) REVERT: D 121 ASP cc_start: 0.8327 (t70) cc_final: 0.7869 (t70) REVERT: D 284 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8607 (ttpp) REVERT: D 367 MET cc_start: 0.8957 (pmm) cc_final: 0.8605 (pmm) REVERT: D 423 ASP cc_start: 0.8469 (p0) cc_final: 0.7857 (t0) REVERT: E 115 GLU cc_start: 0.8620 (tp30) cc_final: 0.8323 (tm-30) REVERT: E 209 TYR cc_start: 0.7702 (m-80) cc_final: 0.7138 (m-80) REVERT: E 363 ASP cc_start: 0.5646 (m-30) cc_final: 0.4843 (t70) REVERT: E 384 THR cc_start: 0.8365 (p) cc_final: 0.8159 (t) REVERT: E 406 MET cc_start: 0.7750 (mtm) cc_final: 0.7090 (mtp) REVERT: E 430 GLU cc_start: 0.8874 (pt0) cc_final: 0.8440 (mt-10) REVERT: E 486 ASP cc_start: 0.8541 (m-30) cc_final: 0.8320 (m-30) REVERT: F 44 ASP cc_start: 0.7664 (m-30) cc_final: 0.7085 (p0) REVERT: F 151 ASN cc_start: 0.8539 (m-40) cc_final: 0.8164 (t0) REVERT: F 232 LYS cc_start: 0.8688 (mppt) cc_final: 0.8274 (mppt) REVERT: F 284 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8036 (tmtt) REVERT: F 380 ASN cc_start: 0.8407 (m-40) cc_final: 0.8013 (t0) REVERT: G 122 GLU cc_start: 0.8851 (tp30) cc_final: 0.7566 (tp30) REVERT: H 38 ILE cc_start: 0.8476 (mp) cc_final: 0.8027 (mt) REVERT: H 131 GLN cc_start: 0.8722 (pp30) cc_final: 0.8472 (pp30) REVERT: H 144 MET cc_start: 0.8370 (ttt) cc_final: 0.7941 (ttt) REVERT: H 168 LEU cc_start: 0.9219 (mp) cc_final: 0.8907 (tp) REVERT: H 284 LYS cc_start: 0.6938 (tptt) cc_final: 0.6616 (pttt) REVERT: H 423 ASP cc_start: 0.8267 (p0) cc_final: 0.7998 (p0) REVERT: H 465 ASP cc_start: 0.9280 (m-30) cc_final: 0.9049 (m-30) REVERT: I 94 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8302 (tm-30) REVERT: I 161 LYS cc_start: 0.8862 (mptt) cc_final: 0.8356 (mtmt) REVERT: I 294 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7322 (tm-30) REVERT: I 406 MET cc_start: 0.4192 (mmm) cc_final: 0.3788 (tpt) REVERT: I 423 ASP cc_start: 0.7748 (p0) cc_final: 0.6724 (t0) REVERT: I 499 LEU cc_start: 0.9069 (mp) cc_final: 0.8834 (mt) REVERT: J 58 ILE cc_start: 0.8484 (pt) cc_final: 0.8117 (mt) REVERT: J 59 LYS cc_start: 0.7095 (mttm) cc_final: 0.6622 (tmtt) REVERT: J 314 TYR cc_start: 0.6741 (m-80) cc_final: 0.6388 (m-80) REVERT: J 520 LYS cc_start: 0.8418 (tptt) cc_final: 0.8186 (tptt) REVERT: J 529 ASN cc_start: 0.8785 (m-40) cc_final: 0.8357 (m110) REVERT: K 114 ASP cc_start: 0.9030 (t0) cc_final: 0.8811 (m-30) REVERT: K 315 MET cc_start: 0.5273 (tmm) cc_final: 0.4958 (tmm) REVERT: K 372 ASN cc_start: 0.8625 (m110) cc_final: 0.8277 (t0) REVERT: K 406 MET cc_start: 0.4733 (tpt) cc_final: 0.3681 (ptm) REVERT: K 410 VAL cc_start: 0.8267 (p) cc_final: 0.7695 (p) REVERT: K 547 GLN cc_start: 0.7714 (pp30) cc_final: 0.7455 (pp30) REVERT: L 19 ASN cc_start: 0.8486 (m-40) cc_final: 0.7850 (t0) REVERT: L 129 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7299 (mm-40) REVERT: L 367 MET cc_start: 0.7781 (ppp) cc_final: 0.7389 (ppp) REVERT: L 501 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7727 (mm-30) REVERT: L 518 MET cc_start: 0.8931 (ttp) cc_final: 0.8446 (ttp) REVERT: M 61 LEU cc_start: 0.9107 (mt) cc_final: 0.8880 (mt) REVERT: M 122 GLU cc_start: 0.8193 (tp30) cc_final: 0.6719 (mt-10) REVERT: M 140 LYS cc_start: 0.8482 (ptpt) cc_final: 0.7898 (mttp) REVERT: M 154 GLN cc_start: 0.7616 (mp-120) cc_final: 0.7038 (mp10) REVERT: M 406 MET cc_start: 0.7566 (tpt) cc_final: 0.7356 (tpt) REVERT: M 472 ASP cc_start: 0.7788 (m-30) cc_final: 0.7487 (m-30) REVERT: M 482 GLN cc_start: 0.8742 (tt0) cc_final: 0.8352 (tt0) REVERT: M 511 TYR cc_start: 0.8130 (m-80) cc_final: 0.7892 (m-80) REVERT: M 525 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8317 (tp40) REVERT: M 537 GLN cc_start: 0.8543 (mp10) cc_final: 0.8180 (mp10) REVERT: N 315 MET cc_start: 0.6660 (ppp) cc_final: 0.6308 (mtt) REVERT: O 88 ASN cc_start: 0.8885 (m-40) cc_final: 0.8476 (t0) REVERT: O 122 GLU cc_start: 0.8580 (tp30) cc_final: 0.7195 (mm-30) REVERT: O 123 ILE cc_start: 0.8442 (mt) cc_final: 0.7684 (mt) REVERT: O 173 PHE cc_start: 0.8478 (t80) cc_final: 0.8168 (t80) REVERT: O 314 TYR cc_start: 0.8652 (m-10) cc_final: 0.8421 (m-10) REVERT: O 315 MET cc_start: 0.7545 (mmp) cc_final: 0.7228 (mmp) REVERT: O 344 LYS cc_start: 0.7227 (tptm) cc_final: 0.6913 (tptp) REVERT: O 390 LYS cc_start: 0.8269 (mmmm) cc_final: 0.8060 (mmtm) REVERT: O 406 MET cc_start: 0.8225 (mmp) cc_final: 0.7987 (mmm) REVERT: a 79 GLU cc_start: 0.8304 (tp30) cc_final: 0.7969 (tp30) REVERT: a 115 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8189 (tp30) REVERT: a 265 ASP cc_start: 0.6551 (p0) cc_final: 0.6180 (p0) REVERT: a 406 MET cc_start: 0.7234 (mmm) cc_final: 0.6504 (mmm) REVERT: a 436 LYS cc_start: 0.7691 (mttt) cc_final: 0.7342 (mptt) REVERT: a 468 ILE cc_start: 0.8516 (mt) cc_final: 0.8222 (mt) REVERT: b 58 ILE cc_start: 0.9014 (pt) cc_final: 0.8789 (pt) REVERT: b 61 LEU cc_start: 0.8947 (mt) cc_final: 0.8661 (mt) REVERT: b 141 ASP cc_start: 0.7820 (m-30) cc_final: 0.7045 (p0) REVERT: c 79 GLU cc_start: 0.8349 (tp30) cc_final: 0.8046 (tp30) REVERT: c 144 MET cc_start: 0.8094 (ttt) cc_final: 0.7758 (ttt) REVERT: c 225 VAL cc_start: 0.8927 (m) cc_final: 0.8703 (p) REVERT: c 392 TYR cc_start: 0.7692 (m-80) cc_final: 0.7329 (m-80) REVERT: c 406 MET cc_start: 0.7644 (tpt) cc_final: 0.7021 (tpp) REVERT: c 478 LEU cc_start: 0.8912 (pp) cc_final: 0.8435 (pp) REVERT: d 21 ASN cc_start: 0.7943 (t0) cc_final: 0.7638 (t0) REVERT: d 39 ASN cc_start: 0.7980 (m-40) cc_final: 0.7181 (m110) REVERT: d 122 GLU cc_start: 0.8883 (tp30) cc_final: 0.8344 (tp30) REVERT: d 255 ASP cc_start: 0.7282 (p0) cc_final: 0.6354 (t0) REVERT: d 280 ARG cc_start: 0.7175 (ptp-110) cc_final: 0.6914 (ptm160) REVERT: d 367 MET cc_start: 0.6487 (tpp) cc_final: 0.6224 (tpp) REVERT: d 470 GLN cc_start: 0.8777 (tt0) cc_final: 0.8556 (tm-30) REVERT: d 501 GLU cc_start: 0.7962 (tt0) cc_final: 0.7647 (mm-30) REVERT: d 518 MET cc_start: 0.9013 (ttp) cc_final: 0.8682 (ttp) REVERT: e 17 ASN cc_start: 0.7684 (m110) cc_final: 0.7426 (m110) REVERT: e 30 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8244 (tm-30) REVERT: e 42 LYS cc_start: 0.7919 (tptt) cc_final: 0.7415 (tmmt) REVERT: e 94 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6149 (tp30) REVERT: e 211 ASP cc_start: 0.7538 (m-30) cc_final: 0.7194 (t70) REVERT: e 334 LEU cc_start: 0.8700 (mt) cc_final: 0.8464 (mt) REVERT: e 406 MET cc_start: 0.4194 (mmm) cc_final: 0.3558 (mmt) REVERT: e 474 PHE cc_start: 0.9246 (t80) cc_final: 0.8438 (t80) REVERT: e 501 GLU cc_start: 0.8108 (tt0) cc_final: 0.7893 (tp30) REVERT: e 514 GLU cc_start: 0.7966 (tp30) cc_final: 0.7757 (tp30) REVERT: f 15 GLN cc_start: 0.8327 (mt0) cc_final: 0.8123 (mm110) REVERT: f 195 THR cc_start: 0.7927 (t) cc_final: 0.7688 (m) REVERT: f 232 LYS cc_start: 0.8098 (tptp) cc_final: 0.7745 (mttm) REVERT: f 459 ASP cc_start: 0.7598 (m-30) cc_final: 0.7370 (m-30) REVERT: g 141 ASP cc_start: 0.8435 (t0) cc_final: 0.8120 (t0) REVERT: g 191 MET cc_start: 0.5052 (tpt) cc_final: 0.4515 (tpt) REVERT: g 278 GLN cc_start: 0.8163 (mp10) cc_final: 0.7428 (pt0) REVERT: g 367 MET cc_start: 0.5823 (mpp) cc_final: 0.4755 (mtt) REVERT: h 31 ARG cc_start: 0.8522 (ttm170) cc_final: 0.7889 (ttp-170) REVERT: h 232 LYS cc_start: 0.7213 (tttp) cc_final: 0.6838 (tppt) REVERT: h 367 MET cc_start: 0.8750 (mpp) cc_final: 0.8388 (mpp) REVERT: h 445 LYS cc_start: 0.8737 (mppt) cc_final: 0.7903 (tptt) outliers start: 2 outliers final: 0 residues processed: 1791 average time/residue: 0.7232 time to fit residues: 2326.6628 Evaluate side-chains 1363 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1363 time to evaluate : 7.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 740 optimal weight: 10.0000 chunk 478 optimal weight: 0.8980 chunk 714 optimal weight: 4.9990 chunk 360 optimal weight: 50.0000 chunk 235 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 761 optimal weight: 0.9990 chunk 815 optimal weight: 8.9990 chunk 591 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 940 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 21 ASN H 52 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN M 48 GLN ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 421 GLN ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 ASN ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 526 GLN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 91126 Z= 0.184 Angle : 0.581 11.434 123878 Z= 0.312 Chirality : 0.040 0.386 15249 Planarity : 0.003 0.048 16583 Dihedral : 4.716 31.616 13110 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.01 % Allowed : 1.05 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.37 (0.08), residues: 12512 helix: 3.07 (0.07), residues: 5327 sheet: -0.31 (0.14), residues: 1327 loop : -2.55 (0.07), residues: 5858 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.001 PHE g 374 TYR 0.016 0.001 TYR A 511 ARG 0.011 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1771 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1770 time to evaluate : 7.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8523 (tt0) cc_final: 0.7909 (tp30) REVERT: A 95 LEU cc_start: 0.9210 (mt) cc_final: 0.8919 (mt) REVERT: A 115 GLU cc_start: 0.8517 (tt0) cc_final: 0.8256 (tt0) REVERT: A 209 TYR cc_start: 0.8190 (m-10) cc_final: 0.7749 (m-10) REVERT: A 358 ASP cc_start: 0.7706 (m-30) cc_final: 0.6586 (p0) REVERT: A 406 MET cc_start: 0.7442 (tpt) cc_final: 0.7160 (tpt) REVERT: A 419 TYR cc_start: 0.7861 (m-80) cc_final: 0.7529 (m-10) REVERT: A 436 LYS cc_start: 0.8109 (mttt) cc_final: 0.7628 (mttp) REVERT: B 122 GLU cc_start: 0.8336 (tp30) cc_final: 0.7722 (tp30) REVERT: B 264 ASP cc_start: 0.7905 (t0) cc_final: 0.7550 (t0) REVERT: B 313 LEU cc_start: 0.8871 (mt) cc_final: 0.8468 (mt) REVERT: B 362 PHE cc_start: 0.3683 (m-80) cc_final: 0.3367 (m-80) REVERT: B 518 MET cc_start: 0.8207 (tpt) cc_final: 0.7976 (tpt) REVERT: C 122 GLU cc_start: 0.8319 (tp30) cc_final: 0.7901 (tt0) REVERT: C 284 LYS cc_start: 0.9278 (mmmt) cc_final: 0.8667 (tmtt) REVERT: C 297 ASN cc_start: 0.8544 (m110) cc_final: 0.8037 (t0) REVERT: C 505 ARG cc_start: 0.8088 (ttm110) cc_final: 0.6989 (ttt180) REVERT: D 121 ASP cc_start: 0.8337 (t70) cc_final: 0.7798 (t0) REVERT: D 284 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8425 (ttpp) REVERT: D 367 MET cc_start: 0.8896 (pmm) cc_final: 0.8558 (pmm) REVERT: D 423 ASP cc_start: 0.8508 (p0) cc_final: 0.7879 (t0) REVERT: E 115 GLU cc_start: 0.8636 (tp30) cc_final: 0.8335 (tm-30) REVERT: E 209 TYR cc_start: 0.7601 (m-80) cc_final: 0.7138 (m-80) REVERT: E 314 TYR cc_start: 0.7830 (m-80) cc_final: 0.7498 (m-10) REVERT: E 406 MET cc_start: 0.7753 (mtm) cc_final: 0.7046 (mpp) REVERT: E 430 GLU cc_start: 0.8858 (pt0) cc_final: 0.8456 (mt-10) REVERT: E 486 ASP cc_start: 0.8566 (m-30) cc_final: 0.8310 (m-30) REVERT: F 44 ASP cc_start: 0.7513 (m-30) cc_final: 0.6920 (p0) REVERT: F 100 SER cc_start: 0.9045 (m) cc_final: 0.8565 (p) REVERT: F 151 ASN cc_start: 0.8471 (m-40) cc_final: 0.8163 (t0) REVERT: F 232 LYS cc_start: 0.8682 (mppt) cc_final: 0.8255 (mppt) REVERT: F 284 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7986 (tmtt) REVERT: F 380 ASN cc_start: 0.8394 (m-40) cc_final: 0.7987 (t0) REVERT: G 436 LYS cc_start: 0.8301 (mppt) cc_final: 0.7441 (tptm) REVERT: H 131 GLN cc_start: 0.8713 (pp30) cc_final: 0.8477 (pp30) REVERT: H 144 MET cc_start: 0.8346 (ttt) cc_final: 0.7863 (ttt) REVERT: H 168 LEU cc_start: 0.9246 (mp) cc_final: 0.8946 (tp) REVERT: H 284 LYS cc_start: 0.6867 (tptt) cc_final: 0.6592 (pttt) REVERT: H 423 ASP cc_start: 0.8283 (p0) cc_final: 0.8024 (p0) REVERT: I 94 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8286 (tm-30) REVERT: I 161 LYS cc_start: 0.8861 (mptt) cc_final: 0.8412 (mtmt) REVERT: I 294 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7308 (tm-30) REVERT: I 406 MET cc_start: 0.4226 (mmm) cc_final: 0.3838 (tpt) REVERT: I 423 ASP cc_start: 0.7718 (p0) cc_final: 0.6757 (t0) REVERT: J 30 GLU cc_start: 0.8877 (tp30) cc_final: 0.8536 (tp30) REVERT: J 59 LYS cc_start: 0.7074 (mttm) cc_final: 0.6659 (tmtt) REVERT: J 314 TYR cc_start: 0.6668 (m-80) cc_final: 0.6291 (m-80) REVERT: J 430 GLU cc_start: 0.8948 (mp0) cc_final: 0.8686 (mp0) REVERT: J 520 LYS cc_start: 0.8192 (tptt) cc_final: 0.7843 (tptt) REVERT: J 529 ASN cc_start: 0.8775 (m-40) cc_final: 0.8356 (m110) REVERT: K 114 ASP cc_start: 0.8994 (t0) cc_final: 0.8765 (m-30) REVERT: K 315 MET cc_start: 0.5281 (tmm) cc_final: 0.4993 (tmm) REVERT: K 372 ASN cc_start: 0.8614 (m110) cc_final: 0.8257 (t0) REVERT: K 406 MET cc_start: 0.4679 (tpt) cc_final: 0.3768 (ptm) REVERT: K 410 VAL cc_start: 0.8296 (p) cc_final: 0.7754 (p) REVERT: K 547 GLN cc_start: 0.7741 (pp30) cc_final: 0.7488 (pp30) REVERT: L 19 ASN cc_start: 0.8451 (m-40) cc_final: 0.7775 (t0) REVERT: L 129 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7308 (mm-40) REVERT: L 274 PHE cc_start: 0.7583 (t80) cc_final: 0.7274 (t80) REVERT: L 501 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7786 (mm-30) REVERT: L 518 MET cc_start: 0.8876 (ttp) cc_final: 0.8350 (ttp) REVERT: M 61 LEU cc_start: 0.9103 (mt) cc_final: 0.8852 (mt) REVERT: M 122 GLU cc_start: 0.8186 (tp30) cc_final: 0.6721 (mt-10) REVERT: M 140 LYS cc_start: 0.8445 (ptpt) cc_final: 0.7874 (mttp) REVERT: M 154 GLN cc_start: 0.7697 (mp-120) cc_final: 0.7078 (mp10) REVERT: M 406 MET cc_start: 0.7596 (tpt) cc_final: 0.7357 (tpt) REVERT: M 472 ASP cc_start: 0.7742 (m-30) cc_final: 0.7455 (m-30) REVERT: M 482 GLN cc_start: 0.8720 (tt0) cc_final: 0.8459 (tt0) REVERT: M 511 TYR cc_start: 0.8111 (m-80) cc_final: 0.7877 (m-80) REVERT: M 525 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8278 (tp40) REVERT: M 537 GLN cc_start: 0.8486 (mp10) cc_final: 0.8005 (mp10) REVERT: N 108 ASP cc_start: 0.8306 (m-30) cc_final: 0.8065 (m-30) REVERT: N 140 LYS cc_start: 0.8409 (mttt) cc_final: 0.8192 (mttp) REVERT: N 315 MET cc_start: 0.6642 (ppp) cc_final: 0.6275 (mtt) REVERT: O 88 ASN cc_start: 0.8847 (m-40) cc_final: 0.8434 (t0) REVERT: O 123 ILE cc_start: 0.8424 (mt) cc_final: 0.7459 (mt) REVERT: O 173 PHE cc_start: 0.8450 (t80) cc_final: 0.8210 (t80) REVERT: O 314 TYR cc_start: 0.8690 (m-10) cc_final: 0.8439 (m-10) REVERT: O 315 MET cc_start: 0.7729 (mmp) cc_final: 0.7381 (mmp) REVERT: O 344 LYS cc_start: 0.7044 (tptm) cc_final: 0.6759 (tptp) REVERT: a 79 GLU cc_start: 0.8237 (tp30) cc_final: 0.7939 (tp30) REVERT: a 241 PHE cc_start: 0.7468 (m-80) cc_final: 0.7158 (m-80) REVERT: a 265 ASP cc_start: 0.6466 (p0) cc_final: 0.6146 (p0) REVERT: a 314 TYR cc_start: 0.6508 (m-10) cc_final: 0.6271 (m-10) REVERT: a 315 MET cc_start: 0.6465 (mmp) cc_final: 0.6243 (mmm) REVERT: a 406 MET cc_start: 0.7211 (mmm) cc_final: 0.6484 (mmm) REVERT: a 430 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6386 (mp0) REVERT: a 436 LYS cc_start: 0.7772 (mttt) cc_final: 0.7362 (mptt) REVERT: b 58 ILE cc_start: 0.9027 (pt) cc_final: 0.8802 (pt) REVERT: b 61 LEU cc_start: 0.8953 (mt) cc_final: 0.8686 (mt) REVERT: b 94 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8267 (tp30) REVERT: b 141 ASP cc_start: 0.7826 (m-30) cc_final: 0.7046 (p0) REVERT: b 423 ASP cc_start: 0.8107 (p0) cc_final: 0.7188 (t0) REVERT: c 79 GLU cc_start: 0.8363 (tp30) cc_final: 0.8084 (tp30) REVERT: c 225 VAL cc_start: 0.9008 (m) cc_final: 0.8790 (p) REVERT: c 392 TYR cc_start: 0.7701 (m-80) cc_final: 0.7353 (m-80) REVERT: c 406 MET cc_start: 0.7628 (tpt) cc_final: 0.7059 (tpp) REVERT: c 478 LEU cc_start: 0.8888 (pp) cc_final: 0.8375 (pp) REVERT: c 532 LEU cc_start: 0.9165 (tt) cc_final: 0.8950 (tt) REVERT: d 21 ASN cc_start: 0.7859 (t0) cc_final: 0.7552 (t0) REVERT: d 39 ASN cc_start: 0.8124 (m-40) cc_final: 0.7299 (m110) REVERT: d 66 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8089 (mtt90) REVERT: d 122 GLU cc_start: 0.8946 (tp30) cc_final: 0.8405 (tp30) REVERT: d 255 ASP cc_start: 0.7201 (p0) cc_final: 0.6239 (t0) REVERT: d 280 ARG cc_start: 0.7154 (ptp-110) cc_final: 0.6887 (ptm160) REVERT: d 367 MET cc_start: 0.6589 (tpp) cc_final: 0.6293 (tpp) REVERT: d 470 GLN cc_start: 0.8750 (tt0) cc_final: 0.8531 (tm-30) REVERT: d 501 GLU cc_start: 0.7945 (tt0) cc_final: 0.7713 (mm-30) REVERT: d 518 MET cc_start: 0.8988 (ttp) cc_final: 0.8679 (ttp) REVERT: e 17 ASN cc_start: 0.7602 (m110) cc_final: 0.7358 (m110) REVERT: e 30 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8247 (tm-30) REVERT: e 42 LYS cc_start: 0.8017 (tptt) cc_final: 0.7422 (tmmt) REVERT: e 94 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6183 (tp30) REVERT: e 129 GLN cc_start: 0.8707 (mt0) cc_final: 0.8362 (mt0) REVERT: e 211 ASP cc_start: 0.7584 (m-30) cc_final: 0.7299 (t70) REVERT: e 315 MET cc_start: 0.7329 (tpp) cc_final: 0.6278 (ttm) REVERT: e 334 LEU cc_start: 0.8661 (mt) cc_final: 0.8403 (mt) REVERT: e 474 PHE cc_start: 0.9249 (t80) cc_final: 0.8366 (t80) REVERT: e 501 GLU cc_start: 0.8099 (tt0) cc_final: 0.7892 (tp30) REVERT: f 195 THR cc_start: 0.7911 (t) cc_final: 0.7659 (m) REVERT: f 232 LYS cc_start: 0.8089 (tptp) cc_final: 0.7749 (mttm) REVERT: f 314 TYR cc_start: 0.6540 (m-80) cc_final: 0.6188 (m-80) REVERT: f 459 ASP cc_start: 0.7551 (m-30) cc_final: 0.7332 (m-30) REVERT: f 501 GLU cc_start: 0.8581 (tp30) cc_final: 0.8310 (tp30) REVERT: g 141 ASP cc_start: 0.8528 (t0) cc_final: 0.8217 (t0) REVERT: g 278 GLN cc_start: 0.7875 (mp10) cc_final: 0.7190 (pt0) REVERT: g 367 MET cc_start: 0.5939 (mpp) cc_final: 0.4968 (mtt) REVERT: g 411 LEU cc_start: 0.7434 (tp) cc_final: 0.7109 (tp) REVERT: g 492 LEU cc_start: 0.9248 (tp) cc_final: 0.8903 (tp) REVERT: h 22 GLN cc_start: 0.8990 (tp40) cc_final: 0.8606 (tp40) REVERT: h 31 ARG cc_start: 0.8385 (ttm170) cc_final: 0.7530 (ttm-80) REVERT: h 232 LYS cc_start: 0.7090 (tttp) cc_final: 0.6760 (tppt) REVERT: h 367 MET cc_start: 0.8743 (mpp) cc_final: 0.8385 (mpp) REVERT: h 445 LYS cc_start: 0.8740 (mppt) cc_final: 0.7917 (tptt) REVERT: h 501 GLU cc_start: 0.8323 (tt0) cc_final: 0.8107 (tt0) outliers start: 1 outliers final: 0 residues processed: 1771 average time/residue: 0.7385 time to fit residues: 2346.8101 Evaluate side-chains 1374 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1374 time to evaluate : 7.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1088 optimal weight: 0.9980 chunk 1146 optimal weight: 4.9990 chunk 1046 optimal weight: 0.9990 chunk 1115 optimal weight: 9.9990 chunk 671 optimal weight: 7.9990 chunk 485 optimal weight: 10.0000 chunk 875 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 1008 optimal weight: 6.9990 chunk 1055 optimal weight: 8.9990 chunk 1111 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 63 GLN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 541 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 21 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 278 GLN ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 ASN ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 526 GLN d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 ASN ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN g 21 ASN ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 91126 Z= 0.190 Angle : 0.586 11.460 123878 Z= 0.314 Chirality : 0.040 0.386 15249 Planarity : 0.003 0.048 16583 Dihedral : 4.675 29.137 13110 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.01 % Allowed : 0.69 % Favored : 99.30 % 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: 0.39 (0.08), residues: 12512 helix: 3.08 (0.07), residues: 5331 sheet: -0.26 (0.14), residues: 1277 loop : -2.53 (0.07), residues: 5904 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE C 374 TYR 0.023 0.001 TYR B 511 ARG 0.009 0.001 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1752 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1751 time to evaluate : 7.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8506 (tt0) cc_final: 0.7905 (tp30) REVERT: A 95 LEU cc_start: 0.9180 (mt) cc_final: 0.8901 (mt) REVERT: A 115 GLU cc_start: 0.8514 (tt0) cc_final: 0.8224 (tt0) REVERT: A 209 TYR cc_start: 0.8193 (m-10) cc_final: 0.7789 (m-10) REVERT: A 358 ASP cc_start: 0.7595 (m-30) cc_final: 0.6657 (p0) REVERT: A 406 MET cc_start: 0.7486 (tpt) cc_final: 0.7208 (tpt) REVERT: A 419 TYR cc_start: 0.7891 (m-80) cc_final: 0.7527 (m-10) REVERT: A 436 LYS cc_start: 0.8112 (mttt) cc_final: 0.7640 (mttp) REVERT: B 122 GLU cc_start: 0.8270 (tp30) cc_final: 0.7735 (tp30) REVERT: B 264 ASP cc_start: 0.7895 (t0) cc_final: 0.7536 (t0) REVERT: B 313 LEU cc_start: 0.8879 (mt) cc_final: 0.8481 (mt) REVERT: B 362 PHE cc_start: 0.3727 (m-80) cc_final: 0.3410 (m-80) REVERT: B 518 MET cc_start: 0.8162 (tpt) cc_final: 0.7846 (tpt) REVERT: C 122 GLU cc_start: 0.8336 (tp30) cc_final: 0.7907 (tt0) REVERT: C 276 ASN cc_start: 0.8683 (m-40) cc_final: 0.8379 (m110) REVERT: C 284 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8653 (tmtt) REVERT: C 297 ASN cc_start: 0.8451 (m110) cc_final: 0.8030 (t0) REVERT: C 505 ARG cc_start: 0.8123 (ttm110) cc_final: 0.6990 (ttt180) REVERT: D 121 ASP cc_start: 0.8292 (t70) cc_final: 0.7730 (t0) REVERT: D 284 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8440 (ttpp) REVERT: D 367 MET cc_start: 0.8900 (pmm) cc_final: 0.8556 (pmm) REVERT: D 423 ASP cc_start: 0.8509 (p0) cc_final: 0.7904 (t0) REVERT: E 115 GLU cc_start: 0.8661 (tp30) cc_final: 0.8336 (tm-30) REVERT: E 209 TYR cc_start: 0.7563 (m-80) cc_final: 0.7116 (m-80) REVERT: E 314 TYR cc_start: 0.7736 (m-80) cc_final: 0.7426 (m-10) REVERT: E 406 MET cc_start: 0.7743 (mtm) cc_final: 0.6994 (mpp) REVERT: E 430 GLU cc_start: 0.8855 (pt0) cc_final: 0.8426 (mt-10) REVERT: E 486 ASP cc_start: 0.8575 (m-30) cc_final: 0.8300 (m-30) REVERT: F 44 ASP cc_start: 0.7580 (m-30) cc_final: 0.7024 (p0) REVERT: F 151 ASN cc_start: 0.8454 (m-40) cc_final: 0.8159 (t0) REVERT: F 232 LYS cc_start: 0.8713 (mppt) cc_final: 0.8285 (mppt) REVERT: F 284 LYS cc_start: 0.8327 (mmmt) cc_final: 0.8092 (tmtt) REVERT: F 380 ASN cc_start: 0.8366 (m-40) cc_final: 0.8012 (t0) REVERT: G 436 LYS cc_start: 0.8289 (mppt) cc_final: 0.7230 (tptm) REVERT: H 131 GLN cc_start: 0.8723 (pp30) cc_final: 0.8478 (pp30) REVERT: H 144 MET cc_start: 0.8360 (ttt) cc_final: 0.7933 (ttt) REVERT: H 168 LEU cc_start: 0.9268 (mp) cc_final: 0.8943 (tp) REVERT: H 284 LYS cc_start: 0.6868 (tptt) cc_final: 0.6596 (pttt) REVERT: I 94 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8241 (tm-30) REVERT: I 122 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7853 (tm-30) REVERT: I 161 LYS cc_start: 0.8854 (mptt) cc_final: 0.8440 (mtmt) REVERT: I 270 ASN cc_start: 0.5791 (t0) cc_final: 0.5412 (t0) REVERT: I 294 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7418 (tm-30) REVERT: I 406 MET cc_start: 0.4158 (mmm) cc_final: 0.3767 (tpt) REVERT: I 423 ASP cc_start: 0.7622 (p0) cc_final: 0.6666 (t0) REVERT: J 59 LYS cc_start: 0.7049 (mttm) cc_final: 0.6642 (tmtt) REVERT: J 194 PHE cc_start: 0.6945 (t80) cc_final: 0.6235 (t80) REVERT: J 314 TYR cc_start: 0.6697 (m-80) cc_final: 0.6294 (m-80) REVERT: J 529 ASN cc_start: 0.8718 (m-40) cc_final: 0.8314 (m110) REVERT: K 114 ASP cc_start: 0.8993 (t0) cc_final: 0.8768 (m-30) REVERT: K 280 ARG cc_start: 0.6675 (mmm160) cc_final: 0.6475 (mmm160) REVERT: K 315 MET cc_start: 0.5232 (tmm) cc_final: 0.4952 (tmm) REVERT: K 372 ASN cc_start: 0.8608 (m110) cc_final: 0.8250 (t0) REVERT: K 406 MET cc_start: 0.4811 (tpt) cc_final: 0.3726 (ptm) REVERT: K 410 VAL cc_start: 0.8332 (p) cc_final: 0.7801 (p) REVERT: K 543 LEU cc_start: 0.8978 (tp) cc_final: 0.8770 (tp) REVERT: K 547 GLN cc_start: 0.7799 (pp30) cc_final: 0.7594 (pp30) REVERT: L 129 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7284 (mm-40) REVERT: L 367 MET cc_start: 0.7759 (ppp) cc_final: 0.7543 (ppp) REVERT: L 501 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7798 (mm-30) REVERT: L 518 MET cc_start: 0.8905 (ttp) cc_final: 0.8605 (ttp) REVERT: M 61 LEU cc_start: 0.9123 (mt) cc_final: 0.8918 (mt) REVERT: M 122 GLU cc_start: 0.8186 (tp30) cc_final: 0.6780 (mt-10) REVERT: M 140 LYS cc_start: 0.8447 (ptpt) cc_final: 0.7890 (mttp) REVERT: M 154 GLN cc_start: 0.7813 (mp-120) cc_final: 0.7215 (mp10) REVERT: M 472 ASP cc_start: 0.7747 (m-30) cc_final: 0.7457 (m-30) REVERT: M 482 GLN cc_start: 0.8664 (tt0) cc_final: 0.8354 (tt0) REVERT: M 511 TYR cc_start: 0.8122 (m-80) cc_final: 0.7870 (m-80) REVERT: M 525 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8272 (tp40) REVERT: M 537 GLN cc_start: 0.8500 (mp10) cc_final: 0.8015 (mp10) REVERT: N 100 SER cc_start: 0.8309 (t) cc_final: 0.8088 (t) REVERT: N 108 ASP cc_start: 0.8302 (m-30) cc_final: 0.8058 (m-30) REVERT: N 114 ASP cc_start: 0.7876 (m-30) cc_final: 0.7674 (m-30) REVERT: N 140 LYS cc_start: 0.8421 (mttt) cc_final: 0.7605 (mmtp) REVERT: O 88 ASN cc_start: 0.8781 (m-40) cc_final: 0.8532 (t0) REVERT: O 122 GLU cc_start: 0.8561 (tp30) cc_final: 0.7273 (mm-30) REVERT: O 123 ILE cc_start: 0.8452 (mt) cc_final: 0.7448 (mt) REVERT: O 173 PHE cc_start: 0.8471 (t80) cc_final: 0.8162 (t80) REVERT: O 314 TYR cc_start: 0.8699 (m-10) cc_final: 0.8431 (m-10) REVERT: O 315 MET cc_start: 0.7737 (mmp) cc_final: 0.7413 (mmp) REVERT: O 344 LYS cc_start: 0.7095 (tptm) cc_final: 0.6778 (tptp) REVERT: O 406 MET cc_start: 0.8216 (mmp) cc_final: 0.7985 (mmp) REVERT: a 79 GLU cc_start: 0.8209 (tp30) cc_final: 0.7900 (tp30) REVERT: a 121 ASP cc_start: 0.8573 (m-30) cc_final: 0.8345 (m-30) REVERT: a 241 PHE cc_start: 0.7513 (m-80) cc_final: 0.7244 (m-80) REVERT: a 265 ASP cc_start: 0.6416 (p0) cc_final: 0.6115 (p0) REVERT: a 314 TYR cc_start: 0.6542 (m-10) cc_final: 0.6286 (m-10) REVERT: a 406 MET cc_start: 0.7286 (mmm) cc_final: 0.6582 (mmm) REVERT: a 430 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6544 (mp0) REVERT: a 436 LYS cc_start: 0.7764 (mttt) cc_final: 0.7360 (mptt) REVERT: b 58 ILE cc_start: 0.9034 (pt) cc_final: 0.8817 (pt) REVERT: b 61 LEU cc_start: 0.8929 (mt) cc_final: 0.8657 (mt) REVERT: b 90 GLN cc_start: 0.7558 (mt0) cc_final: 0.7326 (mt0) REVERT: b 94 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8128 (tp30) REVERT: b 141 ASP cc_start: 0.7835 (m-30) cc_final: 0.7023 (p0) REVERT: b 423 ASP cc_start: 0.8041 (p0) cc_final: 0.7299 (t0) REVERT: c 79 GLU cc_start: 0.8353 (tp30) cc_final: 0.8036 (tp30) REVERT: c 144 MET cc_start: 0.7949 (ttt) cc_final: 0.7347 (ttt) REVERT: c 225 VAL cc_start: 0.9024 (m) cc_final: 0.8803 (p) REVERT: c 392 TYR cc_start: 0.7665 (m-80) cc_final: 0.7338 (m-80) REVERT: c 406 MET cc_start: 0.7642 (tpt) cc_final: 0.7083 (tpp) REVERT: c 478 LEU cc_start: 0.8903 (pp) cc_final: 0.8364 (pp) REVERT: d 21 ASN cc_start: 0.7902 (t0) cc_final: 0.7592 (t0) REVERT: d 39 ASN cc_start: 0.8080 (m-40) cc_final: 0.7157 (m110) REVERT: d 66 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8078 (mtt90) REVERT: d 122 GLU cc_start: 0.8977 (tp30) cc_final: 0.8409 (tp30) REVERT: d 255 ASP cc_start: 0.7263 (p0) cc_final: 0.6270 (t0) REVERT: d 280 ARG cc_start: 0.7143 (ptp-110) cc_final: 0.6876 (ptm160) REVERT: d 367 MET cc_start: 0.6432 (tpp) cc_final: 0.6072 (tpp) REVERT: d 380 ASN cc_start: 0.8463 (m110) cc_final: 0.8137 (p0) REVERT: d 518 MET cc_start: 0.8986 (ttp) cc_final: 0.8694 (ttp) REVERT: e 17 ASN cc_start: 0.7693 (m110) cc_final: 0.7433 (m110) REVERT: e 30 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8222 (tm-30) REVERT: e 42 LYS cc_start: 0.8003 (tptt) cc_final: 0.7404 (tmmt) REVERT: e 94 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6146 (tp30) REVERT: e 211 ASP cc_start: 0.7581 (m-30) cc_final: 0.7338 (t70) REVERT: e 315 MET cc_start: 0.7440 (tpp) cc_final: 0.6400 (mtm) REVERT: e 334 LEU cc_start: 0.8638 (mt) cc_final: 0.8384 (mt) REVERT: e 474 PHE cc_start: 0.9155 (t80) cc_final: 0.8324 (t80) REVERT: e 501 GLU cc_start: 0.8037 (tt0) cc_final: 0.7828 (tp30) REVERT: f 195 THR cc_start: 0.7918 (t) cc_final: 0.7666 (m) REVERT: f 232 LYS cc_start: 0.8141 (tptp) cc_final: 0.7797 (mttm) REVERT: f 314 TYR cc_start: 0.6483 (m-80) cc_final: 0.6151 (m-80) REVERT: f 406 MET cc_start: 0.6293 (tpt) cc_final: 0.5848 (tpt) REVERT: f 501 GLU cc_start: 0.8553 (tp30) cc_final: 0.8257 (tp30) REVERT: g 141 ASP cc_start: 0.8469 (t0) cc_final: 0.8221 (t0) REVERT: g 222 LEU cc_start: 0.8577 (mt) cc_final: 0.8362 (pp) REVERT: g 278 GLN cc_start: 0.7876 (mp10) cc_final: 0.7201 (pt0) REVERT: g 367 MET cc_start: 0.6000 (mpp) cc_final: 0.5030 (mtt) REVERT: g 492 LEU cc_start: 0.9275 (tp) cc_final: 0.8993 (tp) REVERT: h 31 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7470 (ttm-80) REVERT: h 38 ILE cc_start: 0.9316 (mm) cc_final: 0.9094 (mm) REVERT: h 189 LYS cc_start: 0.8370 (tmtt) cc_final: 0.8159 (tptp) REVERT: h 232 LYS cc_start: 0.7147 (tttp) cc_final: 0.6752 (tppt) REVERT: h 379 LYS cc_start: 0.7471 (ttmt) cc_final: 0.6982 (tptt) REVERT: h 445 LYS cc_start: 0.8740 (mppt) cc_final: 0.7928 (tptt) REVERT: h 501 GLU cc_start: 0.8270 (tt0) cc_final: 0.8008 (tt0) outliers start: 1 outliers final: 0 residues processed: 1752 average time/residue: 0.7318 time to fit residues: 2303.7011 Evaluate side-chains 1338 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1338 time to evaluate : 7.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 732 optimal weight: 30.0000 chunk 1179 optimal weight: 0.8980 chunk 719 optimal weight: 6.9990 chunk 559 optimal weight: 10.0000 chunk 820 optimal weight: 2.9990 chunk 1237 optimal weight: 6.9990 chunk 1138 optimal weight: 9.9990 chunk 985 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 761 optimal weight: 0.9980 chunk 604 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 63 GLN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 21 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 21 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 376 ASN ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 270 ASN f 331 GLN f 526 GLN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 ASN g 131 GLN ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 91126 Z= 0.244 Angle : 0.620 11.288 123878 Z= 0.332 Chirality : 0.041 0.391 15249 Planarity : 0.003 0.048 16583 Dihedral : 4.856 34.307 13110 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.98 % Favored : 90.01 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.25 (0.08), residues: 12512 helix: 2.95 (0.07), residues: 5316 sheet: -0.35 (0.14), residues: 1327 loop : -2.58 (0.07), residues: 5869 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE F 374 TYR 0.024 0.002 TYR A 511 ARG 0.012 0.001 ARG L 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1699 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1695 time to evaluate : 7.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8609 (tt0) cc_final: 0.7906 (tp30) REVERT: A 95 LEU cc_start: 0.9243 (mt) cc_final: 0.8938 (mt) REVERT: A 115 GLU cc_start: 0.8534 (tt0) cc_final: 0.8252 (tt0) REVERT: A 209 TYR cc_start: 0.8194 (m-10) cc_final: 0.7764 (m-10) REVERT: A 358 ASP cc_start: 0.7637 (m-30) cc_final: 0.6679 (p0) REVERT: A 406 MET cc_start: 0.7526 (tpt) cc_final: 0.7249 (tpt) REVERT: A 436 LYS cc_start: 0.8123 (mttt) cc_final: 0.7647 (mttp) REVERT: A 470 GLN cc_start: 0.8486 (tt0) cc_final: 0.7900 (tm-30) REVERT: B 105 SER cc_start: 0.8572 (t) cc_final: 0.8316 (t) REVERT: B 122 GLU cc_start: 0.8338 (tp30) cc_final: 0.7773 (tp30) REVERT: B 264 ASP cc_start: 0.7840 (t0) cc_final: 0.7473 (t0) REVERT: B 362 PHE cc_start: 0.3795 (m-80) cc_final: 0.3439 (m-80) REVERT: B 426 ILE cc_start: 0.9271 (mm) cc_final: 0.9022 (mm) REVERT: B 518 MET cc_start: 0.8228 (tpt) cc_final: 0.7998 (tpt) REVERT: C 30 GLU cc_start: 0.7600 (tt0) cc_final: 0.6915 (tp30) REVERT: C 284 LYS cc_start: 0.9278 (mmmt) cc_final: 0.8638 (tmtt) REVERT: C 297 ASN cc_start: 0.8442 (m110) cc_final: 0.8078 (t0) REVERT: C 505 ARG cc_start: 0.8124 (ttm110) cc_final: 0.6980 (ttt180) REVERT: D 121 ASP cc_start: 0.8292 (t70) cc_final: 0.7700 (t0) REVERT: D 284 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8433 (ttpp) REVERT: D 367 MET cc_start: 0.8963 (pmm) cc_final: 0.8625 (pmm) REVERT: D 423 ASP cc_start: 0.8505 (p0) cc_final: 0.7913 (t0) REVERT: E 115 GLU cc_start: 0.8707 (tp30) cc_final: 0.8374 (tp30) REVERT: E 209 TYR cc_start: 0.7582 (m-80) cc_final: 0.7065 (m-80) REVERT: E 314 TYR cc_start: 0.7777 (m-80) cc_final: 0.7457 (m-10) REVERT: E 406 MET cc_start: 0.7851 (mtm) cc_final: 0.6958 (mpp) REVERT: E 430 GLU cc_start: 0.8890 (pt0) cc_final: 0.8443 (mt-10) REVERT: E 486 ASP cc_start: 0.8585 (m-30) cc_final: 0.8304 (m-30) REVERT: F 44 ASP cc_start: 0.7642 (m-30) cc_final: 0.7023 (p0) REVERT: F 151 ASN cc_start: 0.8435 (m-40) cc_final: 0.8190 (t0) REVERT: F 232 LYS cc_start: 0.8769 (mppt) cc_final: 0.8335 (mppt) REVERT: F 284 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8090 (tmtt) REVERT: F 380 ASN cc_start: 0.8332 (m-40) cc_final: 0.7993 (t0) REVERT: G 122 GLU cc_start: 0.8713 (tp30) cc_final: 0.7515 (tp30) REVERT: G 436 LYS cc_start: 0.8325 (mppt) cc_final: 0.7340 (tptm) REVERT: H 131 GLN cc_start: 0.8768 (pp30) cc_final: 0.8493 (pp30) REVERT: H 144 MET cc_start: 0.8396 (ttt) cc_final: 0.7984 (ttt) REVERT: H 168 LEU cc_start: 0.9266 (mp) cc_final: 0.8910 (tp) REVERT: H 284 LYS cc_start: 0.6842 (tptt) cc_final: 0.6638 (pttt) REVERT: H 465 ASP cc_start: 0.9284 (m-30) cc_final: 0.9053 (m-30) REVERT: I 94 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8233 (tm-30) REVERT: I 161 LYS cc_start: 0.8878 (mptt) cc_final: 0.8470 (mtmt) REVERT: I 270 ASN cc_start: 0.5790 (t0) cc_final: 0.5388 (t0) REVERT: I 294 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7446 (tm-30) REVERT: I 406 MET cc_start: 0.4073 (mmm) cc_final: 0.3580 (tpt) REVERT: I 423 ASP cc_start: 0.7598 (p0) cc_final: 0.6795 (t0) REVERT: J 59 LYS cc_start: 0.7053 (mttm) cc_final: 0.6649 (tmtt) REVERT: J 175 VAL cc_start: 0.8747 (p) cc_final: 0.8090 (m) REVERT: J 314 TYR cc_start: 0.6578 (m-80) cc_final: 0.6206 (m-80) REVERT: J 520 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7864 (tptt) REVERT: J 529 ASN cc_start: 0.8707 (m-40) cc_final: 0.8279 (m110) REVERT: K 114 ASP cc_start: 0.8994 (t0) cc_final: 0.8781 (m-30) REVERT: K 315 MET cc_start: 0.5408 (tmm) cc_final: 0.5167 (tmm) REVERT: K 372 ASN cc_start: 0.8624 (m110) cc_final: 0.8226 (t0) REVERT: K 406 MET cc_start: 0.4798 (tpt) cc_final: 0.3687 (ptm) REVERT: K 410 VAL cc_start: 0.8385 (p) cc_final: 0.7856 (p) REVERT: K 547 GLN cc_start: 0.7851 (pp30) cc_final: 0.7573 (pp30) REVERT: L 19 ASN cc_start: 0.8510 (m-40) cc_final: 0.7806 (t0) REVERT: L 129 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7297 (mm-40) REVERT: L 274 PHE cc_start: 0.7811 (t80) cc_final: 0.7565 (t80) REVERT: L 501 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7791 (mm-30) REVERT: L 518 MET cc_start: 0.8933 (ttp) cc_final: 0.8387 (ttp) REVERT: M 61 LEU cc_start: 0.9095 (mt) cc_final: 0.8883 (mt) REVERT: M 122 GLU cc_start: 0.8201 (tp30) cc_final: 0.6724 (mt-10) REVERT: M 140 LYS cc_start: 0.8461 (ptpt) cc_final: 0.7902 (mttp) REVERT: M 408 ASN cc_start: 0.8683 (p0) cc_final: 0.8213 (p0) REVERT: M 482 GLN cc_start: 0.8676 (tt0) cc_final: 0.8362 (tt0) REVERT: M 511 TYR cc_start: 0.8116 (m-80) cc_final: 0.7883 (m-80) REVERT: M 525 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8305 (tp40) REVERT: M 537 GLN cc_start: 0.8501 (mp10) cc_final: 0.8010 (mp10) REVERT: N 18 ILE cc_start: 0.8337 (mm) cc_final: 0.8129 (mm) REVERT: N 94 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7393 (tm-30) REVERT: N 100 SER cc_start: 0.8337 (t) cc_final: 0.8102 (t) REVERT: N 108 ASP cc_start: 0.8488 (m-30) cc_final: 0.8218 (m-30) REVERT: N 114 ASP cc_start: 0.7983 (m-30) cc_final: 0.7753 (m-30) REVERT: N 140 LYS cc_start: 0.8454 (mttt) cc_final: 0.8192 (mttp) REVERT: N 455 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7937 (mm-30) REVERT: O 88 ASN cc_start: 0.8818 (m-40) cc_final: 0.8549 (t0) REVERT: O 123 ILE cc_start: 0.8445 (mt) cc_final: 0.7550 (mt) REVERT: O 173 PHE cc_start: 0.8590 (t80) cc_final: 0.8241 (t80) REVERT: O 314 TYR cc_start: 0.8748 (m-10) cc_final: 0.8470 (m-10) REVERT: O 315 MET cc_start: 0.7840 (mmp) cc_final: 0.7537 (mmp) REVERT: O 406 MET cc_start: 0.7954 (mmp) cc_final: 0.7616 (mmm) REVERT: a 79 GLU cc_start: 0.8259 (tp30) cc_final: 0.7968 (tp30) REVERT: a 121 ASP cc_start: 0.8600 (m-30) cc_final: 0.8378 (m-30) REVERT: a 241 PHE cc_start: 0.7544 (m-80) cc_final: 0.7278 (m-80) REVERT: a 265 ASP cc_start: 0.6434 (p0) cc_final: 0.6145 (p0) REVERT: a 314 TYR cc_start: 0.6497 (m-10) cc_final: 0.6215 (m-10) REVERT: a 362 PHE cc_start: 0.8259 (m-80) cc_final: 0.7895 (m-80) REVERT: a 430 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6546 (mp0) REVERT: a 436 LYS cc_start: 0.7792 (mttt) cc_final: 0.7415 (mptt) REVERT: b 58 ILE cc_start: 0.9009 (pt) cc_final: 0.8752 (pt) REVERT: b 61 LEU cc_start: 0.8966 (mt) cc_final: 0.8677 (mt) REVERT: b 94 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8096 (tp30) REVERT: b 141 ASP cc_start: 0.7843 (m-30) cc_final: 0.6987 (p0) REVERT: b 423 ASP cc_start: 0.8180 (p0) cc_final: 0.7702 (t0) REVERT: c 79 GLU cc_start: 0.8416 (tp30) cc_final: 0.8098 (tp30) REVERT: c 144 MET cc_start: 0.7916 (ttt) cc_final: 0.7397 (ttt) REVERT: c 194 PHE cc_start: 0.8465 (t80) cc_final: 0.8092 (t80) REVERT: c 225 VAL cc_start: 0.9027 (m) cc_final: 0.8784 (p) REVERT: c 348 ILE cc_start: 0.7787 (mm) cc_final: 0.7448 (mm) REVERT: c 392 TYR cc_start: 0.7688 (m-80) cc_final: 0.7314 (m-80) REVERT: c 406 MET cc_start: 0.7738 (tpt) cc_final: 0.7258 (tpp) REVERT: c 478 LEU cc_start: 0.8944 (pp) cc_final: 0.8434 (pp) REVERT: d 21 ASN cc_start: 0.7960 (t0) cc_final: 0.7645 (t0) REVERT: d 39 ASN cc_start: 0.8135 (m-40) cc_final: 0.7127 (m110) REVERT: d 66 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8172 (mtt90) REVERT: d 122 GLU cc_start: 0.8997 (tp30) cc_final: 0.8477 (tp30) REVERT: d 255 ASP cc_start: 0.7331 (p0) cc_final: 0.6398 (t0) REVERT: d 367 MET cc_start: 0.6315 (tpp) cc_final: 0.6015 (tpp) REVERT: d 380 ASN cc_start: 0.8463 (m110) cc_final: 0.8186 (p0) REVERT: e 17 ASN cc_start: 0.7692 (m110) cc_final: 0.7444 (m110) REVERT: e 30 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8215 (tm-30) REVERT: e 42 LYS cc_start: 0.7971 (tptt) cc_final: 0.7385 (tmmt) REVERT: e 94 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6138 (tp30) REVERT: e 211 ASP cc_start: 0.7542 (m-30) cc_final: 0.7333 (t70) REVERT: e 334 LEU cc_start: 0.8632 (mt) cc_final: 0.8325 (mt) REVERT: e 474 PHE cc_start: 0.9155 (t80) cc_final: 0.8390 (t80) REVERT: e 501 GLU cc_start: 0.8090 (tt0) cc_final: 0.7867 (tp30) REVERT: f 232 LYS cc_start: 0.8172 (tptp) cc_final: 0.7850 (mttm) REVERT: f 314 TYR cc_start: 0.6779 (m-80) cc_final: 0.6359 (m-80) REVERT: f 406 MET cc_start: 0.6334 (tpt) cc_final: 0.5934 (tpt) REVERT: f 459 ASP cc_start: 0.7597 (m-30) cc_final: 0.7155 (m-30) REVERT: f 501 GLU cc_start: 0.8542 (tp30) cc_final: 0.8237 (tp30) REVERT: g 141 ASP cc_start: 0.8532 (t0) cc_final: 0.8275 (t0) REVERT: g 278 GLN cc_start: 0.7835 (mp10) cc_final: 0.7160 (pt0) REVERT: g 367 MET cc_start: 0.6121 (mpp) cc_final: 0.4888 (mtt) REVERT: h 31 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7429 (ttm-80) REVERT: h 232 LYS cc_start: 0.7104 (tttp) cc_final: 0.6726 (tppt) REVERT: h 379 LYS cc_start: 0.7616 (ttmt) cc_final: 0.7138 (tptt) REVERT: h 405 TYR cc_start: 0.6641 (m-80) cc_final: 0.6178 (m-10) REVERT: h 445 LYS cc_start: 0.8801 (mppt) cc_final: 0.7924 (tptt) REVERT: h 501 GLU cc_start: 0.8305 (tt0) cc_final: 0.8026 (tt0) outliers start: 4 outliers final: 0 residues processed: 1698 average time/residue: 0.7323 time to fit residues: 2243.4880 Evaluate side-chains 1327 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1327 time to evaluate : 7.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 782 optimal weight: 0.0270 chunk 1049 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 908 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 986 optimal weight: 6.9990 chunk 413 optimal weight: 40.0000 chunk 1013 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 overall best weight: 3.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 63 GLN A 67 ASN A 86 ASN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 21 ASN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN G 491 ASN H 21 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 491 ASN I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 526 GLN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN M 86 ASN ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 541 GLN ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 ASN ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN ** f 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 526 GLN g 16 ASN g 21 ASN ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.154221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121109 restraints weight = 190603.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120906 restraints weight = 130816.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121332 restraints weight = 107085.809| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 91126 Z= 0.232 Angle : 0.615 11.509 123878 Z= 0.329 Chirality : 0.041 0.384 15249 Planarity : 0.003 0.048 16583 Dihedral : 4.859 43.388 13110 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.19 (0.08), residues: 12512 helix: 2.91 (0.07), residues: 5346 sheet: -0.46 (0.14), residues: 1369 loop : -2.64 (0.07), residues: 5797 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE F 374 TYR 0.025 0.001 TYR A 511 ARG 0.009 0.001 ARG I 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31424.06 seconds wall clock time: 548 minutes 4.64 seconds (32884.64 seconds total)