Starting phenix.real_space_refine on Thu Mar 21 20:20:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udq_20743/03_2024/6udq_20743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udq_20743/03_2024/6udq_20743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udq_20743/03_2024/6udq_20743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udq_20743/03_2024/6udq_20743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udq_20743/03_2024/6udq_20743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udq_20743/03_2024/6udq_20743_updated.pdb" } resolution = 3.27 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= 0.059 sd= 3.203 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: 5 Type Number sf(0) Gaussians P 80 5.49 5 S 172 5.16 5 C 19292 2.51 5 N 5324 2.21 5 O 6140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 355": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 355": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31008 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "B" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "C" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'ATP': 2, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'ATP': 2, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 15.01, per 1000 atoms: 0.48 Number of scatterers: 31008 At special positions: 0 Unit cell: (151.25, 152.076, 116.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 80 15.00 O 6140 8.00 N 5324 7.00 C 19292 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 5.7 seconds 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 149 helices and 48 sheets defined 31.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'I' and resid 2 through 5 No H-bonds generated for 'chain 'I' and resid 2 through 5' Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.602A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.677A pdb=" N ARG A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.628A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.909A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.682A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.671A pdb=" N TYR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.548A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 128 through 136 Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.751A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA E 264 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.985A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.631A pdb=" N LYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 316 " --> pdb=" O ASN E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 354 removed outlier: 3.773A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.609A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.517A pdb=" N ARG B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.598A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.874A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.642A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.791A pdb=" N TYR B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'F' and resid 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.524A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 107 removed outlier: 3.539A pdb=" N GLU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 136 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.638A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA F 264 " --> pdb=" O ASP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.978A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.650A pdb=" N LYS F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 354 removed outlier: 3.622A pdb=" N TYR F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'K' and resid 2 through 5 No H-bonds generated for 'chain 'K' and resid 2 through 5' Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.576A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.543A pdb=" N ARG C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.613A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.894A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.645A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.731A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.555A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 removed outlier: 3.711A pdb=" N LYS G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 136 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.646A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA G 264 " --> pdb=" O ASP G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.899A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.646A pdb=" N LYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 354 removed outlier: 3.817A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'L' and resid 2 through 5 No H-bonds generated for 'chain 'L' and resid 2 through 5' Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.659A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.506A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.681A pdb=" N ARG D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.552A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.919A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.712A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 354 removed outlier: 3.668A pdb=" N TYR D 348 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 removed outlier: 3.500A pdb=" N LEU D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.639A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 129 through 136 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 203 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.706A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA H 264 " --> pdb=" O ASP H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.923A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.641A pdb=" N LYS H 311 " --> pdb=" O ALA H 307 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 316 " --> pdb=" O ASN H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 354 removed outlier: 3.661A pdb=" N TYR H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.156A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.384A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 408 through 412 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'A' and resid 209 through 212 removed outlier: 3.918A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.131A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 383 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 120 through 122 Processing sheet with id= J, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.533A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= L, first strand: chain 'E' and resid 209 through 212 removed outlier: 3.534A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.147A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.398A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 408 through 412 Processing sheet with id= Q, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= R, first strand: chain 'B' and resid 209 through 212 removed outlier: 3.961A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.678A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 320 through 323 removed outlier: 7.531A pdb=" N VAL F 323 " --> pdb=" O PRO F 360 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE F 362 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR F 383 " --> pdb=" O ALA F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= W, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= X, first strand: chain 'F' and resid 209 through 212 removed outlier: 3.527A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.135A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 187 through 189 removed outlier: 3.559A pdb=" N ILE C 222 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.302A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= AD, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.530A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.104A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AH, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.550A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AJ, first strand: chain 'G' and resid 209 through 212 Processing sheet with id= AK, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.153A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'D' and resid 187 through 189 removed outlier: 3.571A pdb=" N ILE D 222 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.383A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= AP, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.621A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.175A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 120 through 122 Processing sheet with id= AT, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.692A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'H' and resid 400 through 403 Processing sheet with id= AV, first strand: chain 'H' and resid 209 through 212 removed outlier: 3.555A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2040 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: 8.83 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5227 1.31 - 1.43: 7594 1.43 - 1.56: 18260 1.56 - 1.69: 167 1.69 - 1.82: 280 Bond restraints: 31528 Sorted by residual: bond pdb=" C2' GTP C 602 " pdb=" C3' GTP C 602 " ideal model delta sigma weight residual 1.524 1.228 0.296 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C2' GTP D 602 " pdb=" C3' GTP D 602 " ideal model delta sigma weight residual 1.524 1.228 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' GTP B 602 " pdb=" C3' GTP B 602 " ideal model delta sigma weight residual 1.524 1.228 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' GTP A 602 " pdb=" C3' GTP A 602 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C2' GTP E 602 " pdb=" C3' GTP E 602 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.17e+02 ... (remaining 31523 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.25: 619 105.25 - 112.99: 17238 112.99 - 120.74: 14649 120.74 - 128.48: 10053 128.48 - 136.23: 197 Bond angle restraints: 42756 Sorted by residual: angle pdb=" PB ATP A 605 " pdb=" O3B ATP A 605 " pdb=" PG ATP A 605 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PB ATP C 605 " pdb=" O3B ATP C 605 " pdb=" PG ATP C 605 " ideal model delta sigma weight residual 139.87 119.57 20.30 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP B 604 " pdb=" O3B ATP B 604 " pdb=" PG ATP B 604 " ideal model delta sigma weight residual 139.87 119.80 20.07 1.00e+00 1.00e+00 4.03e+02 angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP A 604 " pdb=" O3B ATP A 604 " pdb=" PG ATP A 604 " ideal model delta sigma weight residual 139.87 120.64 19.23 1.00e+00 1.00e+00 3.70e+02 ... (remaining 42751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 18785 35.48 - 70.97: 255 70.97 - 106.45: 27 106.45 - 141.94: 32 141.94 - 177.42: 17 Dihedral angle restraints: 19116 sinusoidal: 7876 harmonic: 11240 Sorted by residual: dihedral pdb=" CA SER L 11 " pdb=" C SER L 11 " pdb=" N TYR L 12 " pdb=" CA TYR L 12 " ideal model delta harmonic sigma weight residual 180.00 134.87 45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CA SER I 11 " pdb=" C SER I 11 " pdb=" N TYR I 12 " pdb=" CA TYR I 12 " ideal model delta harmonic sigma weight residual 180.00 134.95 45.05 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA SER J 11 " pdb=" C SER J 11 " pdb=" N TYR J 12 " pdb=" CA TYR J 12 " ideal model delta harmonic sigma weight residual 180.00 135.50 44.50 0 5.00e+00 4.00e-02 7.92e+01 ... (remaining 19113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3434 0.057 - 0.113: 1101 0.113 - 0.170: 280 0.170 - 0.227: 43 0.227 - 0.283: 10 Chirality restraints: 4868 Sorted by residual: chirality pdb=" C3' IMP F 601 " pdb=" C2' IMP F 601 " pdb=" C4' IMP F 601 " pdb=" O3' IMP F 601 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' IMP G 601 " pdb=" C2' IMP G 601 " pdb=" C4' IMP G 601 " pdb=" O3' IMP G 601 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB THR D 74 " pdb=" CA THR D 74 " pdb=" OG1 THR D 74 " pdb=" CG2 THR D 74 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4865 not shown) Planarity restraints: 5360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 169 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLU H 169 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU H 169 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU H 170 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 169 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C GLU E 169 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU E 169 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU E 170 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 169 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C GLU F 169 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU F 169 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU F 170 " -0.013 2.00e-02 2.50e+03 ... (remaining 5357 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6166 2.77 - 3.30: 28044 3.30 - 3.84: 52244 3.84 - 4.37: 63556 4.37 - 4.90: 106336 Nonbonded interactions: 256346 Sorted by model distance: nonbonded pdb=" OG1 THR C 193 " pdb=" OE1 GLU C 196 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR B 193 " pdb=" OE1 GLU B 196 " model vdw 2.248 2.440 nonbonded pdb=" OD1 ASP C 146 " pdb=" OG SER C 152 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR D 193 " pdb=" OE1 GLU D 196 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP D 146 " pdb=" OG SER D 152 " model vdw 2.268 2.440 ... (remaining 256341 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' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'B' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'C' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'D' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'E' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'F' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'G' and (resid 12 through 514 or resid 601 through 603)) selection = (chain 'H' and (resid 12 through 514 or resid 601 through 603)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.640 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 74.720 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.014 0.296 31528 Z= 0.893 Angle : 1.187 20.322 42756 Z= 0.724 Chirality : 0.060 0.283 4868 Planarity : 0.006 0.056 5360 Dihedral : 15.049 177.420 11940 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.09 % Allowed : 3.75 % Favored : 95.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 1.52 % Twisted General : 0.11 % 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: -3.91 (0.11), residues: 3916 helix: -3.28 (0.09), residues: 1348 sheet: -2.22 (0.20), residues: 544 loop : -2.14 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 466 PHE 0.026 0.003 PHE A 401 TYR 0.038 0.003 TYR F 400 ARG 0.019 0.002 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 809 time to evaluate : 3.320 Fit side-chains REVERT: A 34 ASP cc_start: 0.8493 (m-30) cc_final: 0.8190 (m-30) REVERT: A 116 THR cc_start: 0.8543 (m) cc_final: 0.8248 (m) REVERT: A 179 MET cc_start: 0.8173 (pp-130) cc_final: 0.7566 (pp-130) REVERT: A 512 ARG cc_start: 0.7007 (ttt-90) cc_final: 0.6280 (tpt90) REVERT: E 124 LYS cc_start: 0.7358 (tppt) cc_final: 0.6980 (tptp) REVERT: E 265 GLN cc_start: 0.8620 (tt0) cc_final: 0.8351 (mt0) REVERT: E 330 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9071 (pp) REVERT: E 352 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8347 (tm-30) REVERT: E 412 ARG cc_start: 0.8117 (ptt-90) cc_final: 0.7655 (ptt180) REVERT: E 438 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7257 (mttm) REVERT: B 116 THR cc_start: 0.8528 (m) cc_final: 0.8254 (m) REVERT: B 119 VAL cc_start: 0.8445 (m) cc_final: 0.8221 (p) REVERT: B 152 SER cc_start: 0.6602 (t) cc_final: 0.6247 (t) REVERT: B 179 MET cc_start: 0.8301 (pp-130) cc_final: 0.7546 (ppp) REVERT: B 181 LYS cc_start: 0.7406 (mppt) cc_final: 0.7202 (mmmt) REVERT: F 179 MET cc_start: 0.8191 (ppp) cc_final: 0.7807 (ppp) REVERT: F 265 GLN cc_start: 0.8678 (tt0) cc_final: 0.8168 (mt0) REVERT: F 330 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8831 (pp) REVERT: F 412 ARG cc_start: 0.8015 (ptt-90) cc_final: 0.7740 (ptt180) REVERT: C 59 ILE cc_start: 0.8588 (mm) cc_final: 0.8381 (mt) REVERT: C 82 MET cc_start: 0.8964 (mmm) cc_final: 0.8577 (mmt) REVERT: C 152 SER cc_start: 0.7041 (t) cc_final: 0.6811 (t) REVERT: C 192 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7456 (tp) REVERT: C 512 ARG cc_start: 0.6815 (ttt-90) cc_final: 0.6164 (tpt90) REVERT: G 109 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7729 (mttt) REVERT: G 179 MET cc_start: 0.8324 (ppp) cc_final: 0.8001 (ppp) REVERT: G 206 LYS cc_start: 0.7725 (tptt) cc_final: 0.7499 (tppt) REVERT: G 265 GLN cc_start: 0.8689 (tt0) cc_final: 0.8320 (mt0) REVERT: G 330 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8938 (pp) REVERT: G 411 TYR cc_start: 0.9065 (t80) cc_final: 0.8705 (t80) REVERT: G 412 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7564 (ptt180) REVERT: G 480 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8565 (mtm-85) REVERT: D 179 MET cc_start: 0.8079 (pp-130) cc_final: 0.7683 (pp-130) REVERT: D 192 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7478 (tp) REVERT: H 94 ASN cc_start: 0.8842 (t0) cc_final: 0.8432 (t0) REVERT: H 124 LYS cc_start: 0.7361 (tppt) cc_final: 0.6944 (tptp) REVERT: H 179 MET cc_start: 0.8312 (ppp) cc_final: 0.7692 (ppp) REVERT: H 184 ASP cc_start: 0.7958 (p0) cc_final: 0.7455 (p0) REVERT: H 265 GLN cc_start: 0.8759 (tt0) cc_final: 0.8147 (mt0) REVERT: H 330 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8866 (pp) REVERT: H 412 ARG cc_start: 0.8171 (ptt-90) cc_final: 0.7750 (ptt180) outliers start: 35 outliers final: 6 residues processed: 820 average time/residue: 0.4495 time to fit residues: 566.5019 Evaluate side-chains 552 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 540 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 330 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.5980 chunk 294 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 198 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 226 optimal weight: 0.7980 chunk 352 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 368 GLN A 466 HIS E 112 GLN E 253 HIS ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 253 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 466 HIS B 469 GLN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN C 48 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS C 368 GLN C 466 HIS G 94 ASN G 102 ASN G 171 HIS G 253 HIS ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS D 253 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 466 HIS H 94 ASN H 102 ASN H 112 GLN H 253 HIS ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 368 GLN H 466 HIS H 504 HIS H 507 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31528 Z= 0.183 Angle : 0.592 8.578 42756 Z= 0.293 Chirality : 0.044 0.195 4868 Planarity : 0.004 0.047 5360 Dihedral : 16.991 171.933 4835 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.13 % Allowed : 10.36 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.52 (0.12), residues: 3916 helix: -1.67 (0.12), residues: 1356 sheet: -1.61 (0.21), residues: 548 loop : -1.61 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 507 PHE 0.017 0.001 PHE F 99 TYR 0.011 0.001 TYR F 400 ARG 0.004 0.001 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 578 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7730 (t0) REVERT: A 192 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7558 (tp) REVERT: E 124 LYS cc_start: 0.7398 (tppt) cc_final: 0.7060 (tptp) REVERT: E 184 ASP cc_start: 0.8078 (p0) cc_final: 0.7527 (p0) REVERT: E 265 GLN cc_start: 0.8463 (tt0) cc_final: 0.8207 (mt0) REVERT: E 330 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9061 (pp) REVERT: E 352 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8360 (tm-30) REVERT: E 383 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8789 (p) REVERT: E 412 ARG cc_start: 0.8124 (ptt-90) cc_final: 0.7690 (ptt180) REVERT: E 420 MET cc_start: 0.5976 (mpp) cc_final: 0.5761 (mpp) REVERT: E 438 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7281 (mttm) REVERT: B 34 ASP cc_start: 0.8213 (m-30) cc_final: 0.7949 (m-30) REVERT: B 274 ASP cc_start: 0.8666 (t70) cc_final: 0.8455 (t0) REVERT: F 94 ASN cc_start: 0.8850 (t160) cc_final: 0.8368 (t0) REVERT: F 109 LYS cc_start: 0.7729 (mttt) cc_final: 0.7401 (mttt) REVERT: F 184 ASP cc_start: 0.8182 (p0) cc_final: 0.7813 (p0) REVERT: F 265 GLN cc_start: 0.8547 (tt0) cc_final: 0.8059 (mt0) REVERT: F 330 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8847 (pp) REVERT: F 412 ARG cc_start: 0.7985 (ptt-90) cc_final: 0.7619 (ptt180) REVERT: C 28 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7629 (t0) REVERT: C 119 VAL cc_start: 0.8293 (m) cc_final: 0.8078 (p) REVERT: C 179 MET cc_start: 0.8056 (pp-130) cc_final: 0.7477 (pp-130) REVERT: C 192 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7485 (tp) REVERT: C 216 ASP cc_start: 0.7640 (m-30) cc_final: 0.7300 (t0) REVERT: G 36 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8153 (pp) REVERT: G 265 GLN cc_start: 0.8558 (tt0) cc_final: 0.8200 (mt0) REVERT: G 330 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8921 (pp) REVERT: G 412 ARG cc_start: 0.7856 (ptt-90) cc_final: 0.7461 (ptt180) REVERT: G 420 MET cc_start: 0.5808 (mpp) cc_final: 0.5570 (mpp) REVERT: D 80 ILE cc_start: 0.9007 (pp) cc_final: 0.8791 (mt) REVERT: D 103 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: D 179 MET cc_start: 0.8144 (pp-130) cc_final: 0.7282 (pp-130) REVERT: D 192 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7495 (tp) REVERT: H 159 SER cc_start: 0.9064 (m) cc_final: 0.8218 (t) REVERT: H 179 MET cc_start: 0.8455 (ppp) cc_final: 0.7855 (ppp) REVERT: H 184 ASP cc_start: 0.7926 (p0) cc_final: 0.7407 (p0) REVERT: H 252 THR cc_start: 0.8880 (p) cc_final: 0.8596 (p) REVERT: H 265 GLN cc_start: 0.8488 (tt0) cc_final: 0.7941 (mt0) REVERT: H 330 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8855 (pp) REVERT: H 412 ARG cc_start: 0.8113 (ptt-90) cc_final: 0.7743 (ptt180) outliers start: 101 outliers final: 43 residues processed: 633 average time/residue: 0.4168 time to fit residues: 423.9778 Evaluate side-chains 562 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 507 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 368 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 293 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 352 optimal weight: 0.6980 chunk 381 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 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 202 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN E 334 GLN E 368 GLN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 HIS C 171 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 171 HIS G 334 GLN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN H 112 GLN H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31528 Z= 0.359 Angle : 0.661 8.079 42756 Z= 0.326 Chirality : 0.048 0.177 4868 Planarity : 0.004 0.051 5360 Dihedral : 16.605 178.352 4834 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.37 % Allowed : 11.82 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.01 (0.13), residues: 3916 helix: -1.05 (0.13), residues: 1368 sheet: -1.59 (0.21), residues: 512 loop : -1.40 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 466 PHE 0.014 0.002 PHE D 282 TYR 0.017 0.002 TYR F 400 ARG 0.007 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 537 time to evaluate : 3.468 Fit side-chains REVERT: A 28 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7785 (t0) REVERT: A 150 MET cc_start: 0.7613 (mmm) cc_final: 0.7030 (tpt) REVERT: A 179 MET cc_start: 0.8173 (pp-130) cc_final: 0.7209 (pp-130) REVERT: A 410 LYS cc_start: 0.7423 (mtpp) cc_final: 0.7033 (mmtt) REVERT: E 36 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8125 (pp) REVERT: E 94 ASN cc_start: 0.9068 (t0) cc_final: 0.8766 (t0) REVERT: E 124 LYS cc_start: 0.7673 (tppt) cc_final: 0.7171 (tptp) REVERT: E 149 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7157 (mtp85) REVERT: E 179 MET cc_start: 0.8519 (ppp) cc_final: 0.8319 (ppp) REVERT: E 184 ASP cc_start: 0.8146 (p0) cc_final: 0.7577 (p0) REVERT: E 306 THR cc_start: 0.9247 (p) cc_final: 0.9021 (t) REVERT: E 322 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8086 (ttt180) REVERT: E 330 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9124 (pp) REVERT: E 352 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8509 (tm-30) REVERT: E 368 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7565 (mp-120) REVERT: E 412 ARG cc_start: 0.8141 (ptt-90) cc_final: 0.7852 (ptt180) REVERT: E 438 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7257 (mttp) REVERT: B 28 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7676 (t0) REVERT: B 62 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8706 (mmtm) REVERT: B 199 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7068 (pt0) REVERT: F 65 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8503 (pp) REVERT: F 82 MET cc_start: 0.8855 (tpp) cc_final: 0.8312 (mmt) REVERT: F 94 ASN cc_start: 0.9078 (t0) cc_final: 0.8813 (t0) REVERT: F 109 LYS cc_start: 0.8058 (mttt) cc_final: 0.7563 (mtpt) REVERT: F 179 MET cc_start: 0.8455 (ppp) cc_final: 0.8144 (ppp) REVERT: F 184 ASP cc_start: 0.8215 (p0) cc_final: 0.7856 (p0) REVERT: F 265 GLN cc_start: 0.8569 (tt0) cc_final: 0.8156 (mt0) REVERT: F 330 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8932 (pp) REVERT: F 412 ARG cc_start: 0.7996 (ptt-90) cc_final: 0.7633 (ptt180) REVERT: C 28 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7668 (t0) REVERT: C 34 ASP cc_start: 0.8407 (m-30) cc_final: 0.8196 (m-30) REVERT: C 163 ILE cc_start: 0.8823 (pt) cc_final: 0.8399 (mt) REVERT: C 404 ASP cc_start: 0.5951 (t0) cc_final: 0.5698 (t0) REVERT: C 410 LYS cc_start: 0.7455 (mtpp) cc_final: 0.6940 (mmtt) REVERT: C 498 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.5691 (mp10) REVERT: G 36 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8248 (pp) REVERT: G 94 ASN cc_start: 0.9083 (t0) cc_final: 0.8811 (t0) REVERT: G 179 MET cc_start: 0.8497 (ppp) cc_final: 0.8084 (ppp) REVERT: G 265 GLN cc_start: 0.8581 (tt0) cc_final: 0.8362 (mt0) REVERT: G 330 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8924 (pp) REVERT: G 412 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7683 (ptt180) REVERT: D 103 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: D 179 MET cc_start: 0.8333 (pp-130) cc_final: 0.7342 (pp-130) REVERT: D 513 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6666 (mp) REVERT: H 36 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8222 (pp) REVERT: H 159 SER cc_start: 0.9167 (m) cc_final: 0.8366 (t) REVERT: H 179 MET cc_start: 0.8413 (ppp) cc_final: 0.7527 (ppp) REVERT: H 184 ASP cc_start: 0.7995 (p0) cc_final: 0.7462 (p0) REVERT: H 252 THR cc_start: 0.8958 (p) cc_final: 0.8689 (p) REVERT: H 265 GLN cc_start: 0.8541 (tt0) cc_final: 0.8241 (mt0) REVERT: H 330 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8931 (pp) REVERT: H 352 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8480 (tm-30) REVERT: H 412 ARG cc_start: 0.8153 (ptt-90) cc_final: 0.7761 (ptt180) outliers start: 141 outliers final: 83 residues processed: 626 average time/residue: 0.4064 time to fit residues: 407.9316 Evaluate side-chains 595 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 496 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 375 optimal weight: 0.0970 chunk 185 optimal weight: 0.5980 chunk 335 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 265 GLN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 HIS ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN G 94 ASN G 303 ASN G 343 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 334 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31528 Z= 0.156 Angle : 0.551 7.877 42756 Z= 0.268 Chirality : 0.043 0.153 4868 Planarity : 0.003 0.043 5360 Dihedral : 15.614 178.088 4830 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.07 % Allowed : 14.17 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3916 helix: -0.42 (0.14), residues: 1368 sheet: -1.35 (0.21), residues: 556 loop : -1.22 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 507 PHE 0.013 0.001 PHE A 514 TYR 0.010 0.001 TYR H 459 ARG 0.004 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 562 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 150 MET cc_start: 0.7513 (mmm) cc_final: 0.7027 (tpt) REVERT: A 170 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.4832 (tt0) REVERT: A 179 MET cc_start: 0.8208 (pp-130) cc_final: 0.7244 (pp-130) REVERT: A 410 LYS cc_start: 0.7374 (mtpp) cc_final: 0.6907 (mmtt) REVERT: E 36 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7754 (pp) REVERT: E 94 ASN cc_start: 0.8993 (t0) cc_final: 0.8656 (t0) REVERT: E 149 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7112 (mtp85) REVERT: E 179 MET cc_start: 0.8358 (ppp) cc_final: 0.7702 (ppp) REVERT: E 184 ASP cc_start: 0.8094 (p0) cc_final: 0.7531 (p0) REVERT: E 330 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9113 (pp) REVERT: E 352 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8516 (tm-30) REVERT: E 385 MET cc_start: 0.8423 (ttp) cc_final: 0.7969 (ttm) REVERT: E 412 ARG cc_start: 0.8075 (ptt-90) cc_final: 0.7627 (ptt180) REVERT: E 438 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7207 (mttp) REVERT: B 28 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7656 (t0) REVERT: B 62 LYS cc_start: 0.8905 (mmtp) cc_final: 0.8680 (mmtm) REVERT: B 150 MET cc_start: 0.7586 (mmm) cc_final: 0.7177 (tpt) REVERT: B 167 LYS cc_start: 0.6344 (tppt) cc_final: 0.5420 (tttp) REVERT: B 199 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7006 (pt0) REVERT: B 274 ASP cc_start: 0.8675 (t70) cc_final: 0.8475 (t0) REVERT: F 82 MET cc_start: 0.8743 (tpp) cc_final: 0.8016 (tpt) REVERT: F 94 ASN cc_start: 0.8920 (t160) cc_final: 0.8684 (t0) REVERT: F 109 LYS cc_start: 0.7985 (mttt) cc_final: 0.7500 (mttt) REVERT: F 179 MET cc_start: 0.8429 (ppp) cc_final: 0.8053 (ppp) REVERT: F 184 ASP cc_start: 0.8121 (p0) cc_final: 0.7773 (p0) REVERT: F 265 GLN cc_start: 0.8486 (tt0) cc_final: 0.8172 (mt0) REVERT: F 364 ASP cc_start: 0.8176 (p0) cc_final: 0.7893 (p0) REVERT: F 412 ARG cc_start: 0.7900 (ptt-90) cc_final: 0.7598 (ptt180) REVERT: C 136 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.8225 (tpp-160) REVERT: C 163 ILE cc_start: 0.8852 (pt) cc_final: 0.8526 (mt) REVERT: C 206 LYS cc_start: 0.7938 (mmmm) cc_final: 0.7491 (mmmm) REVERT: C 404 ASP cc_start: 0.5894 (t0) cc_final: 0.5666 (t0) REVERT: C 410 LYS cc_start: 0.7439 (mtpp) cc_final: 0.7054 (mmtt) REVERT: G 94 ASN cc_start: 0.8934 (t160) cc_final: 0.8640 (t0) REVERT: G 179 MET cc_start: 0.8539 (ppp) cc_final: 0.8172 (ppp) REVERT: G 265 GLN cc_start: 0.8481 (tt0) cc_final: 0.8230 (mt0) REVERT: G 330 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8876 (pp) REVERT: G 385 MET cc_start: 0.8791 (ttp) cc_final: 0.8473 (ttm) REVERT: G 412 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.7422 (ptt180) REVERT: D 28 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7550 (t0) REVERT: D 62 LYS cc_start: 0.8907 (mmtp) cc_final: 0.8689 (mmtm) REVERT: D 103 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: D 150 MET cc_start: 0.7611 (mmm) cc_final: 0.7146 (tpt) REVERT: D 179 MET cc_start: 0.8287 (pp-130) cc_final: 0.7190 (pp-130) REVERT: D 206 LYS cc_start: 0.8001 (tppt) cc_final: 0.7570 (mmmm) REVERT: D 410 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7370 (tppt) REVERT: H 36 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7860 (pp) REVERT: H 159 SER cc_start: 0.9076 (m) cc_final: 0.8148 (t) REVERT: H 179 MET cc_start: 0.8319 (ppp) cc_final: 0.7558 (ppp) REVERT: H 184 ASP cc_start: 0.8021 (p0) cc_final: 0.7476 (p0) REVERT: H 252 THR cc_start: 0.8758 (p) cc_final: 0.8464 (p) REVERT: H 334 GLN cc_start: 0.8396 (mt0) cc_final: 0.8160 (mt0) REVERT: H 385 MET cc_start: 0.8439 (ttp) cc_final: 0.8062 (ttm) REVERT: H 412 ARG cc_start: 0.8037 (ptt-90) cc_final: 0.7662 (ptt180) outliers start: 99 outliers final: 55 residues processed: 617 average time/residue: 0.4074 time to fit residues: 405.6510 Evaluate side-chains 575 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 511 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 5 optimal weight: 0.0000 chunk 279 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 320 optimal weight: 0.0060 chunk 259 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 336 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 265 GLN E 334 GLN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 253 HIS ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31528 Z= 0.146 Angle : 0.539 9.979 42756 Z= 0.261 Chirality : 0.043 0.149 4868 Planarity : 0.003 0.041 5360 Dihedral : 14.735 173.775 4826 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.29 % Allowed : 15.17 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3916 helix: -0.00 (0.15), residues: 1364 sheet: -1.15 (0.21), residues: 556 loop : -1.08 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.023 0.001 PHE F 99 TYR 0.009 0.001 TYR H 459 ARG 0.006 0.000 ARG E 512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 532 time to evaluate : 3.593 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7732 (t0) REVERT: A 150 MET cc_start: 0.7417 (mmm) cc_final: 0.6879 (tpt) REVERT: A 170 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.4711 (mt-10) REVERT: A 179 MET cc_start: 0.8242 (pp-130) cc_final: 0.7267 (pp-130) REVERT: A 410 LYS cc_start: 0.7385 (mtpp) cc_final: 0.6943 (mmtt) REVERT: A 412 ARG cc_start: 0.7817 (ptt-90) cc_final: 0.7586 (ptt-90) REVERT: E 94 ASN cc_start: 0.9025 (t0) cc_final: 0.8682 (t0) REVERT: E 149 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7056 (mtp85) REVERT: E 179 MET cc_start: 0.8327 (ppp) cc_final: 0.7644 (ppp) REVERT: E 184 ASP cc_start: 0.8061 (p0) cc_final: 0.7482 (p0) REVERT: E 385 MET cc_start: 0.8525 (ttp) cc_final: 0.8061 (ttm) REVERT: E 412 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7667 (ptt180) REVERT: E 438 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7220 (mttp) REVERT: B 28 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 62 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8673 (mmtm) REVERT: B 150 MET cc_start: 0.7543 (mmm) cc_final: 0.7115 (tpt) REVERT: B 199 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6991 (pt0) REVERT: B 410 LYS cc_start: 0.7624 (ttmm) cc_final: 0.6920 (mmtt) REVERT: F 36 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8222 (pp) REVERT: F 94 ASN cc_start: 0.8961 (t160) cc_final: 0.8737 (t0) REVERT: F 109 LYS cc_start: 0.7929 (mttt) cc_final: 0.7455 (mttt) REVERT: F 179 MET cc_start: 0.8415 (ppp) cc_final: 0.8026 (ppp) REVERT: F 184 ASP cc_start: 0.8134 (p0) cc_final: 0.7576 (p0) REVERT: F 265 GLN cc_start: 0.8404 (tt0) cc_final: 0.8170 (mt0) REVERT: F 412 ARG cc_start: 0.7915 (ptt-90) cc_final: 0.7591 (ptt180) REVERT: C 12 TYR cc_start: 0.5119 (OUTLIER) cc_final: 0.4528 (t80) REVERT: C 136 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.8220 (tpp-160) REVERT: C 150 MET cc_start: 0.6712 (mmm) cc_final: 0.6141 (tpt) REVERT: C 163 ILE cc_start: 0.8860 (pt) cc_final: 0.8593 (mt) REVERT: C 206 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7555 (mmmm) REVERT: C 410 LYS cc_start: 0.7461 (mtpp) cc_final: 0.7119 (mmtt) REVERT: G 36 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7817 (pp) REVERT: G 94 ASN cc_start: 0.8960 (t160) cc_final: 0.8702 (t0) REVERT: G 179 MET cc_start: 0.8504 (ppp) cc_final: 0.8279 (ppp) REVERT: G 330 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8848 (pp) REVERT: G 412 ARG cc_start: 0.7698 (ptt-90) cc_final: 0.7380 (ptt180) REVERT: D 28 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7550 (t0) REVERT: D 62 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8679 (mmtm) REVERT: D 103 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: D 150 MET cc_start: 0.7519 (mmm) cc_final: 0.6801 (tpt) REVERT: D 153 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7779 (mmm-85) REVERT: D 179 MET cc_start: 0.8326 (pp-130) cc_final: 0.7069 (pp-130) REVERT: D 274 ASP cc_start: 0.8753 (t70) cc_final: 0.8531 (t0) REVERT: D 410 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7283 (tppt) REVERT: H 36 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7921 (pp) REVERT: H 159 SER cc_start: 0.9010 (m) cc_final: 0.8042 (t) REVERT: H 179 MET cc_start: 0.8293 (ppp) cc_final: 0.7440 (ppp) REVERT: H 184 ASP cc_start: 0.7953 (p0) cc_final: 0.7392 (p0) REVERT: H 252 THR cc_start: 0.8648 (p) cc_final: 0.8342 (p) REVERT: H 385 MET cc_start: 0.8539 (ttp) cc_final: 0.8122 (ttm) REVERT: H 412 ARG cc_start: 0.8014 (ptt-90) cc_final: 0.7725 (ptt180) outliers start: 106 outliers final: 64 residues processed: 594 average time/residue: 0.4242 time to fit residues: 399.8321 Evaluate side-chains 568 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 494 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 2.9990 chunk 337 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 375 optimal weight: 3.9990 chunk 311 optimal weight: 0.0670 chunk 173 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 202 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN H 112 GLN H 253 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31528 Z= 0.173 Angle : 0.550 9.214 42756 Z= 0.267 Chirality : 0.043 0.145 4868 Planarity : 0.003 0.039 5360 Dihedral : 14.453 176.290 4824 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.29 % Allowed : 16.00 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.94 (0.13), residues: 3916 helix: 0.16 (0.15), residues: 1364 sheet: -0.89 (0.22), residues: 516 loop : -1.06 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.027 0.001 PHE H 139 TYR 0.010 0.001 TYR F 459 ARG 0.005 0.000 ARG E 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 514 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 150 MET cc_start: 0.7377 (mmm) cc_final: 0.6800 (tpt) REVERT: A 170 GLU cc_start: 0.5671 (OUTLIER) cc_final: 0.4812 (mt-10) REVERT: A 179 MET cc_start: 0.8282 (pp-130) cc_final: 0.7283 (pp-130) REVERT: A 410 LYS cc_start: 0.7379 (mtpp) cc_final: 0.6959 (mmtt) REVERT: E 36 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7750 (pp) REVERT: E 94 ASN cc_start: 0.9053 (t0) cc_final: 0.8657 (t0) REVERT: E 149 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.6974 (mtp85) REVERT: E 179 MET cc_start: 0.8374 (ppp) cc_final: 0.7737 (ppp) REVERT: E 184 ASP cc_start: 0.8002 (p0) cc_final: 0.7383 (p0) REVERT: E 412 ARG cc_start: 0.8096 (ptt-90) cc_final: 0.7702 (ptt180) REVERT: E 438 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7248 (mttp) REVERT: B 28 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7621 (t0) REVERT: B 62 LYS cc_start: 0.8927 (mmtp) cc_final: 0.8677 (mmtm) REVERT: B 150 MET cc_start: 0.7518 (mmm) cc_final: 0.7030 (tpt) REVERT: B 163 ILE cc_start: 0.8874 (pt) cc_final: 0.8520 (mt) REVERT: B 199 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6973 (pt0) REVERT: B 410 LYS cc_start: 0.7632 (ttmm) cc_final: 0.6928 (mmtt) REVERT: F 36 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8168 (pp) REVERT: F 94 ASN cc_start: 0.8981 (t160) cc_final: 0.8743 (t0) REVERT: F 109 LYS cc_start: 0.7948 (mttt) cc_final: 0.7563 (tttt) REVERT: F 179 MET cc_start: 0.8437 (ppp) cc_final: 0.8014 (ppp) REVERT: F 184 ASP cc_start: 0.8124 (p0) cc_final: 0.7550 (p0) REVERT: F 412 ARG cc_start: 0.7941 (ptt-90) cc_final: 0.7648 (ptt180) REVERT: C 136 ARG cc_start: 0.8448 (tpp-160) cc_final: 0.8211 (tpp-160) REVERT: C 150 MET cc_start: 0.6644 (mmm) cc_final: 0.6148 (tpt) REVERT: C 163 ILE cc_start: 0.8885 (pt) cc_final: 0.8637 (mt) REVERT: C 199 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6927 (pt0) REVERT: C 410 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7115 (mmtt) REVERT: G 36 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7808 (pp) REVERT: G 94 ASN cc_start: 0.8988 (t160) cc_final: 0.8687 (t0) REVERT: G 330 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8828 (pp) REVERT: G 412 ARG cc_start: 0.7719 (ptt-90) cc_final: 0.7371 (ptt180) REVERT: D 28 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7570 (t0) REVERT: D 62 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8684 (mmtm) REVERT: D 103 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: D 150 MET cc_start: 0.7494 (mmm) cc_final: 0.6880 (tpt) REVERT: D 153 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.8049 (mmm-85) REVERT: D 179 MET cc_start: 0.8326 (pp-130) cc_final: 0.7054 (pp-130) REVERT: D 199 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6731 (pt0) REVERT: D 410 LYS cc_start: 0.7559 (ttmm) cc_final: 0.7333 (tppt) REVERT: H 36 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7856 (pp) REVERT: H 159 SER cc_start: 0.8970 (m) cc_final: 0.8029 (t) REVERT: H 179 MET cc_start: 0.8210 (ppp) cc_final: 0.7320 (ppp) REVERT: H 184 ASP cc_start: 0.7929 (p0) cc_final: 0.7386 (p0) REVERT: H 252 THR cc_start: 0.8651 (p) cc_final: 0.8341 (p) REVERT: H 412 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7731 (ptt180) outliers start: 106 outliers final: 81 residues processed: 576 average time/residue: 0.4051 time to fit residues: 375.8118 Evaluate side-chains 576 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 485 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 213 optimal weight: 0.6980 chunk 274 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 316 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 373 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN F 303 ASN C 202 GLN G 265 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN H 112 GLN H 253 HIS H 334 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31528 Z= 0.161 Angle : 0.546 9.128 42756 Z= 0.264 Chirality : 0.043 0.154 4868 Planarity : 0.003 0.038 5360 Dihedral : 14.120 173.571 4824 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.57 % Allowed : 16.53 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.80 (0.13), residues: 3916 helix: 0.30 (0.15), residues: 1360 sheet: -0.92 (0.23), residues: 492 loop : -0.96 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.023 0.001 PHE H 139 TYR 0.009 0.001 TYR D 509 ARG 0.004 0.000 ARG E 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 504 time to evaluate : 3.628 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 150 MET cc_start: 0.7326 (mmm) cc_final: 0.6730 (tpt) REVERT: A 170 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.4833 (mt-10) REVERT: A 179 MET cc_start: 0.8265 (pp-130) cc_final: 0.7266 (pp-130) REVERT: A 216 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.7056 (t0) REVERT: A 410 LYS cc_start: 0.7401 (mtpp) cc_final: 0.7012 (mmtt) REVERT: E 36 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7753 (pp) REVERT: E 94 ASN cc_start: 0.9058 (t0) cc_final: 0.8665 (t0) REVERT: E 149 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.6900 (mtp85) REVERT: E 179 MET cc_start: 0.8227 (ppp) cc_final: 0.7787 (ppp) REVERT: E 184 ASP cc_start: 0.7991 (p0) cc_final: 0.7360 (p0) REVERT: E 330 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8968 (pp) REVERT: E 412 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7714 (ptt180) REVERT: E 438 LYS cc_start: 0.7723 (mtmm) cc_final: 0.7265 (mttp) REVERT: B 28 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7603 (t0) REVERT: B 150 MET cc_start: 0.7401 (mmm) cc_final: 0.6940 (tpt) REVERT: B 163 ILE cc_start: 0.8861 (pt) cc_final: 0.8459 (mt) REVERT: B 199 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7020 (pt0) REVERT: B 322 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (tmm-80) REVERT: B 410 LYS cc_start: 0.7625 (ttmm) cc_final: 0.6923 (mmtt) REVERT: F 36 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8181 (pp) REVERT: F 94 ASN cc_start: 0.8967 (t160) cc_final: 0.8732 (t0) REVERT: F 109 LYS cc_start: 0.7997 (mttt) cc_final: 0.7510 (mttt) REVERT: F 179 MET cc_start: 0.8435 (ppp) cc_final: 0.7569 (ppp) REVERT: F 184 ASP cc_start: 0.8086 (p0) cc_final: 0.7519 (p0) REVERT: F 265 GLN cc_start: 0.8649 (mt0) cc_final: 0.8410 (mt0) REVERT: F 412 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7627 (ptt180) REVERT: C 12 TYR cc_start: 0.5102 (OUTLIER) cc_final: 0.4669 (t80) REVERT: C 150 MET cc_start: 0.6629 (mmm) cc_final: 0.6117 (tpt) REVERT: C 410 LYS cc_start: 0.7380 (mtpp) cc_final: 0.6854 (mmtt) REVERT: G 36 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7872 (pp) REVERT: G 94 ASN cc_start: 0.9000 (t160) cc_final: 0.8703 (t0) REVERT: G 179 MET cc_start: 0.8180 (ppp) cc_final: 0.7889 (ppp) REVERT: G 330 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8813 (pp) REVERT: G 412 ARG cc_start: 0.7727 (ptt-90) cc_final: 0.7406 (ptt180) REVERT: D 28 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7552 (t0) REVERT: D 62 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8692 (mmtm) REVERT: D 103 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 150 MET cc_start: 0.7382 (mmm) cc_final: 0.6781 (tpt) REVERT: D 153 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.8013 (mmm-85) REVERT: D 179 MET cc_start: 0.8310 (pp-130) cc_final: 0.7049 (pp-130) REVERT: D 199 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6690 (pt0) REVERT: D 410 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7332 (tppt) REVERT: H 36 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8072 (pp) REVERT: H 159 SER cc_start: 0.8929 (m) cc_final: 0.7981 (t) REVERT: H 179 MET cc_start: 0.8149 (ppp) cc_final: 0.7379 (ppp) REVERT: H 184 ASP cc_start: 0.7950 (p0) cc_final: 0.7371 (p0) REVERT: H 252 THR cc_start: 0.8630 (p) cc_final: 0.8318 (p) REVERT: H 412 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7768 (ptt180) outliers start: 115 outliers final: 85 residues processed: 574 average time/residue: 0.4033 time to fit residues: 372.6317 Evaluate side-chains 581 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 482 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 223 optimal weight: 0.0070 chunk 112 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 293 optimal weight: 0.6980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 343 GLN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 253 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31528 Z= 0.275 Angle : 0.600 9.237 42756 Z= 0.293 Chirality : 0.046 0.161 4868 Planarity : 0.003 0.038 5360 Dihedral : 13.987 176.780 4824 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.66 % Allowed : 16.66 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.13), residues: 3916 helix: 0.20 (0.15), residues: 1364 sheet: -1.01 (0.23), residues: 488 loop : -0.93 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 466 PHE 0.029 0.001 PHE E 139 TYR 0.013 0.001 TYR D 348 ARG 0.004 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 515 time to evaluate : 3.375 Fit side-chains REVERT: A 28 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7765 (t0) REVERT: A 150 MET cc_start: 0.7329 (mmm) cc_final: 0.6779 (tpt) REVERT: A 179 MET cc_start: 0.8306 (pp-130) cc_final: 0.7284 (pp-130) REVERT: A 216 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6923 (t0) REVERT: A 410 LYS cc_start: 0.7377 (mtpp) cc_final: 0.7094 (mmtt) REVERT: E 36 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7989 (pp) REVERT: E 94 ASN cc_start: 0.9121 (t0) cc_final: 0.8724 (t0) REVERT: E 149 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.6912 (mtp85) REVERT: E 179 MET cc_start: 0.8173 (ppp) cc_final: 0.7694 (ppp) REVERT: E 184 ASP cc_start: 0.8052 (p0) cc_final: 0.7411 (p0) REVERT: E 330 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9014 (pp) REVERT: E 412 ARG cc_start: 0.8114 (ptt-90) cc_final: 0.7725 (ptt180) REVERT: E 438 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7341 (mttp) REVERT: B 28 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7626 (t0) REVERT: B 150 MET cc_start: 0.7395 (mmm) cc_final: 0.6940 (tpt) REVERT: B 163 ILE cc_start: 0.8837 (pt) cc_final: 0.8485 (mt) REVERT: F 36 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8406 (pp) REVERT: F 82 MET cc_start: 0.8832 (tpp) cc_final: 0.8582 (mmt) REVERT: F 94 ASN cc_start: 0.9114 (t0) cc_final: 0.8832 (t0) REVERT: F 109 LYS cc_start: 0.7980 (mttt) cc_final: 0.7501 (mttt) REVERT: F 179 MET cc_start: 0.8481 (ppp) cc_final: 0.8167 (ppp) REVERT: F 265 GLN cc_start: 0.8698 (mt0) cc_final: 0.8483 (mt0) REVERT: F 412 ARG cc_start: 0.7995 (ptt-90) cc_final: 0.7673 (ptt180) REVERT: C 12 TYR cc_start: 0.5243 (OUTLIER) cc_final: 0.4751 (t80) REVERT: C 150 MET cc_start: 0.6695 (mmm) cc_final: 0.6197 (tpt) REVERT: C 163 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8111 (tt) REVERT: C 404 ASP cc_start: 0.5671 (t0) cc_final: 0.5212 (t70) REVERT: C 410 LYS cc_start: 0.7404 (mtpp) cc_final: 0.6832 (mmtt) REVERT: G 36 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8144 (pp) REVERT: G 94 ASN cc_start: 0.9144 (t0) cc_final: 0.8791 (t0) REVERT: G 179 MET cc_start: 0.8180 (ppp) cc_final: 0.7906 (ppp) REVERT: G 330 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8818 (pp) REVERT: G 412 ARG cc_start: 0.7835 (ptt-90) cc_final: 0.7481 (ptt180) REVERT: D 28 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7546 (t0) REVERT: D 103 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: D 150 MET cc_start: 0.7354 (mmm) cc_final: 0.6760 (tpt) REVERT: D 153 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8087 (mmm-85) REVERT: D 179 MET cc_start: 0.8388 (pp-130) cc_final: 0.7127 (pp-130) REVERT: D 199 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6727 (pt0) REVERT: D 410 LYS cc_start: 0.7692 (ttmm) cc_final: 0.7484 (tppt) REVERT: H 36 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8245 (pp) REVERT: H 159 SER cc_start: 0.8963 (m) cc_final: 0.8069 (t) REVERT: H 179 MET cc_start: 0.8236 (ppp) cc_final: 0.7407 (ppp) REVERT: H 184 ASP cc_start: 0.8001 (p0) cc_final: 0.7409 (p0) REVERT: H 252 THR cc_start: 0.8806 (p) cc_final: 0.8520 (p) REVERT: H 412 ARG cc_start: 0.8125 (ptt-90) cc_final: 0.7789 (ptt180) outliers start: 118 outliers final: 89 residues processed: 587 average time/residue: 0.4022 time to fit residues: 383.4764 Evaluate side-chains 596 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 494 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 0.2980 chunk 358 optimal weight: 3.9990 chunk 326 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 347 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN B 202 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 253 HIS H 265 GLN H 334 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31528 Z= 0.183 Angle : 0.567 9.082 42756 Z= 0.274 Chirality : 0.044 0.162 4868 Planarity : 0.003 0.039 5360 Dihedral : 13.612 169.413 4824 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.47 % Allowed : 17.06 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.13), residues: 3916 helix: 0.36 (0.15), residues: 1364 sheet: -0.90 (0.23), residues: 492 loop : -0.91 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 466 PHE 0.024 0.001 PHE E 139 TYR 0.010 0.001 TYR F 459 ARG 0.006 0.000 ARG F 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 503 time to evaluate : 3.505 Fit side-chains REVERT: A 28 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7739 (t0) REVERT: A 150 MET cc_start: 0.7254 (mmm) cc_final: 0.6805 (tpt) REVERT: A 179 MET cc_start: 0.8308 (pp-130) cc_final: 0.7298 (pp-130) REVERT: A 216 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7018 (t0) REVERT: A 410 LYS cc_start: 0.7528 (mtpp) cc_final: 0.7204 (mmtt) REVERT: E 36 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7811 (pp) REVERT: E 94 ASN cc_start: 0.9084 (t0) cc_final: 0.8674 (t0) REVERT: E 149 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.6830 (mtp85) REVERT: E 179 MET cc_start: 0.8093 (ppp) cc_final: 0.7719 (ppp) REVERT: E 184 ASP cc_start: 0.7995 (p0) cc_final: 0.7343 (p0) REVERT: E 330 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9014 (pp) REVERT: E 412 ARG cc_start: 0.8074 (ptt-90) cc_final: 0.7690 (ptt180) REVERT: E 438 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7327 (mttp) REVERT: B 28 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7614 (t0) REVERT: B 150 MET cc_start: 0.7344 (mmm) cc_final: 0.6843 (tpt) REVERT: B 163 ILE cc_start: 0.8827 (pt) cc_final: 0.8475 (mt) REVERT: B 410 LYS cc_start: 0.7664 (ttmm) cc_final: 0.6967 (mmtt) REVERT: F 36 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8239 (pp) REVERT: F 94 ASN cc_start: 0.9066 (t0) cc_final: 0.8784 (t0) REVERT: F 109 LYS cc_start: 0.7836 (mttt) cc_final: 0.7356 (mttt) REVERT: F 179 MET cc_start: 0.8429 (ppp) cc_final: 0.8090 (ppp) REVERT: F 412 ARG cc_start: 0.7992 (ptt-90) cc_final: 0.7680 (ptt180) REVERT: C 12 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4728 (t80) REVERT: C 150 MET cc_start: 0.6608 (mmm) cc_final: 0.6203 (tpt) REVERT: C 163 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8125 (tt) REVERT: C 198 ASN cc_start: 0.8495 (m-40) cc_final: 0.8195 (m-40) REVERT: C 404 ASP cc_start: 0.5787 (t0) cc_final: 0.5271 (t70) REVERT: C 410 LYS cc_start: 0.7366 (mtpp) cc_final: 0.6835 (mmtt) REVERT: G 36 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7822 (pp) REVERT: G 94 ASN cc_start: 0.9111 (t0) cc_final: 0.8720 (t0) REVERT: G 330 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8783 (pp) REVERT: G 412 ARG cc_start: 0.7807 (ptt-90) cc_final: 0.7463 (ptt180) REVERT: D 28 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7521 (t0) REVERT: D 103 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: D 150 MET cc_start: 0.7319 (mmm) cc_final: 0.7084 (tpt) REVERT: D 153 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: D 179 MET cc_start: 0.8344 (pp-130) cc_final: 0.8142 (ppp) REVERT: D 199 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6668 (pt0) REVERT: H 36 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7866 (pp) REVERT: H 159 SER cc_start: 0.8978 (m) cc_final: 0.8049 (t) REVERT: H 179 MET cc_start: 0.8168 (ppp) cc_final: 0.7445 (ppp) REVERT: H 184 ASP cc_start: 0.7954 (p0) cc_final: 0.7351 (p0) REVERT: H 252 THR cc_start: 0.8772 (p) cc_final: 0.8489 (p) REVERT: H 265 GLN cc_start: 0.8633 (mt0) cc_final: 0.8376 (mt0) REVERT: H 412 ARG cc_start: 0.8124 (ptt-90) cc_final: 0.7774 (ptt180) outliers start: 112 outliers final: 87 residues processed: 568 average time/residue: 0.4121 time to fit residues: 376.8415 Evaluate side-chains 582 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 482 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 0.4980 chunk 368 optimal weight: 1.9990 chunk 224 optimal weight: 0.2980 chunk 174 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 386 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 307 optimal weight: 0.0270 chunk 31 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN G 94 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN H 112 GLN H 253 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31528 Z= 0.154 Angle : 0.559 8.995 42756 Z= 0.270 Chirality : 0.043 0.160 4868 Planarity : 0.003 0.041 5360 Dihedral : 13.213 176.962 4824 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.26 % Allowed : 17.52 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.60 (0.14), residues: 3916 helix: 0.50 (0.15), residues: 1360 sheet: -0.80 (0.24), residues: 472 loop : -0.87 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.000 HIS E 507 PHE 0.025 0.001 PHE D 139 TYR 0.009 0.001 TYR F 459 ARG 0.005 0.000 ARG E 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 499 time to evaluate : 3.896 Fit side-chains REVERT: A 71 ASP cc_start: 0.8669 (p0) cc_final: 0.8350 (p0) REVERT: A 150 MET cc_start: 0.7203 (mmm) cc_final: 0.6967 (tpt) REVERT: A 179 MET cc_start: 0.8275 (pp-130) cc_final: 0.7266 (pp-130) REVERT: A 216 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6988 (t0) REVERT: A 410 LYS cc_start: 0.7553 (mtpp) cc_final: 0.7203 (mmtt) REVERT: E 36 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7727 (pp) REVERT: E 94 ASN cc_start: 0.9079 (t0) cc_final: 0.8660 (t0) REVERT: E 149 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.6779 (mtp85) REVERT: E 179 MET cc_start: 0.8043 (ppp) cc_final: 0.7711 (ppp) REVERT: E 184 ASP cc_start: 0.7992 (p0) cc_final: 0.7316 (p0) REVERT: E 330 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8976 (pp) REVERT: E 412 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7656 (ptt180) REVERT: E 438 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7316 (mttp) REVERT: B 28 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7631 (t0) REVERT: B 150 MET cc_start: 0.7320 (mmm) cc_final: 0.6712 (tpt) REVERT: B 163 ILE cc_start: 0.8875 (pt) cc_final: 0.8592 (mt) REVERT: B 410 LYS cc_start: 0.7557 (ttmm) cc_final: 0.6886 (mmtt) REVERT: B 512 ARG cc_start: 0.7543 (tpt-90) cc_final: 0.7336 (tpt90) REVERT: F 36 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8232 (pp) REVERT: F 82 MET cc_start: 0.8760 (tpp) cc_final: 0.8516 (mmt) REVERT: F 94 ASN cc_start: 0.9044 (t0) cc_final: 0.8759 (t0) REVERT: F 109 LYS cc_start: 0.7808 (mttt) cc_final: 0.7339 (mttt) REVERT: F 179 MET cc_start: 0.8384 (ppp) cc_final: 0.8088 (ppp) REVERT: F 184 ASP cc_start: 0.7918 (p0) cc_final: 0.7422 (p0) REVERT: F 412 ARG cc_start: 0.7951 (ptt-90) cc_final: 0.7622 (ptt180) REVERT: F 513 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7127 (mt) REVERT: C 12 TYR cc_start: 0.4978 (OUTLIER) cc_final: 0.4690 (t80) REVERT: C 150 MET cc_start: 0.6548 (mmm) cc_final: 0.6205 (tpt) REVERT: C 163 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8183 (tt) REVERT: C 410 LYS cc_start: 0.7373 (mtpp) cc_final: 0.6871 (mmtt) REVERT: C 498 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6589 (mt0) REVERT: G 36 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7717 (pp) REVERT: G 94 ASN cc_start: 0.9036 (t160) cc_final: 0.8715 (t0) REVERT: G 330 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8752 (pp) REVERT: D 28 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7514 (t0) REVERT: D 103 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: D 150 MET cc_start: 0.7290 (mmm) cc_final: 0.7000 (tpt) REVERT: D 153 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8103 (mmm-85) REVERT: D 179 MET cc_start: 0.8332 (pp-130) cc_final: 0.8125 (ppp) REVERT: D 199 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6599 (pt0) REVERT: D 512 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6513 (ttt-90) REVERT: H 36 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7881 (pp) REVERT: H 150 MET cc_start: 0.7233 (ptm) cc_final: 0.6991 (ppp) REVERT: H 159 SER cc_start: 0.8991 (m) cc_final: 0.8085 (t) REVERT: H 179 MET cc_start: 0.8117 (ppp) cc_final: 0.7372 (ppp) REVERT: H 184 ASP cc_start: 0.7927 (p0) cc_final: 0.7328 (p0) REVERT: H 252 THR cc_start: 0.8730 (p) cc_final: 0.8440 (p) REVERT: H 265 GLN cc_start: 0.8599 (mt0) cc_final: 0.8348 (mt0) REVERT: H 412 ARG cc_start: 0.8105 (ptt-90) cc_final: 0.7767 (ptt180) outliers start: 105 outliers final: 77 residues processed: 558 average time/residue: 0.4023 time to fit residues: 361.9054 Evaluate side-chains 570 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 478 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 512 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 316 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN H 112 GLN H 253 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117072 restraints weight = 37546.772| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.42 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31528 Z= 0.169 Angle : 0.562 9.005 42756 Z= 0.272 Chirality : 0.043 0.159 4868 Planarity : 0.003 0.040 5360 Dihedral : 13.084 175.054 4824 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.23 % Allowed : 17.77 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.55 (0.14), residues: 3916 helix: 0.56 (0.15), residues: 1360 sheet: -0.81 (0.24), residues: 472 loop : -0.84 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 507 PHE 0.024 0.001 PHE D 139 TYR 0.009 0.001 TYR C 509 ARG 0.006 0.000 ARG E 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7937.92 seconds wall clock time: 143 minutes 13.16 seconds (8593.16 seconds total)