Starting phenix.real_space_refine on Tue Feb 13 21:18:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/02_2024/5wq9_6677_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/02_2024/5wq9_6677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/02_2024/5wq9_6677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/02_2024/5wq9_6677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/02_2024/5wq9_6677_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq9_6677/02_2024/5wq9_6677_neut.pdb" } resolution = 4.22 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 35205 2.51 5 N 9840 2.21 5 O 11100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 598": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 521": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E ARG 598": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 604": "NH1" <-> "NH2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 521": "NH1" <-> "NH2" Residue "G ARG 598": "NH1" <-> "NH2" Residue "G ARG 604": "NH1" <-> "NH2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 604": "NH1" <-> "NH2" Residue "I GLU 253": "OE1" <-> "OE2" Residue "I ARG 517": "NH1" <-> "NH2" Residue "I ARG 521": "NH1" <-> "NH2" Residue "I ARG 598": "NH1" <-> "NH2" Residue "I ARG 604": "NH1" <-> "NH2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J ARG 517": "NH1" <-> "NH2" Residue "J ARG 521": "NH1" <-> "NH2" Residue "J ARG 598": "NH1" <-> "NH2" Residue "J ARG 604": "NH1" <-> "NH2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K ARG 517": "NH1" <-> "NH2" Residue "K ARG 521": "NH1" <-> "NH2" Residue "K ARG 598": "NH1" <-> "NH2" Residue "K ARG 604": "NH1" <-> "NH2" Residue "L GLU 253": "OE1" <-> "OE2" Residue "L ARG 517": "NH1" <-> "NH2" Residue "L ARG 521": "NH1" <-> "NH2" Residue "L ARG 598": "NH1" <-> "NH2" Residue "L ARG 604": "NH1" <-> "NH2" Residue "M GLU 253": "OE1" <-> "OE2" Residue "M ARG 517": "NH1" <-> "NH2" Residue "M ARG 521": "NH1" <-> "NH2" Residue "M ARG 598": "NH1" <-> "NH2" Residue "M ARG 604": "NH1" <-> "NH2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N ARG 517": "NH1" <-> "NH2" Residue "N ARG 521": "NH1" <-> "NH2" Residue "N ARG 598": "NH1" <-> "NH2" Residue "N ARG 604": "NH1" <-> "NH2" Residue "O GLU 253": "OE1" <-> "OE2" Residue "O ARG 517": "NH1" <-> "NH2" Residue "O ARG 521": "NH1" <-> "NH2" Residue "O ARG 598": "NH1" <-> "NH2" Residue "O ARG 604": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 56340 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "B" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "C" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "D" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "E" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "F" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "G" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "H" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "I" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "J" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "K" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "L" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "M" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "N" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Chain: "O" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3756 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 479} Chain breaks: 5 Time building chain proxies: 20.84, per 1000 atoms: 0.37 Number of scatterers: 56340 At special positions: 0 Unit cell: (175.56, 174.24, 203.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 11100 8.00 N 9840 7.00 C 35205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.39 Conformation dependent library (CDL) restraints added in 7.9 seconds 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13770 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 62 sheets defined 33.3% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL A 623 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL B 623 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA D 592 " --> pdb=" O ASP D 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL D 623 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN D 645 " --> pdb=" O ALA D 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU E 308 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 397 through 405 Processing helix chain 'E' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA E 592 " --> pdb=" O ASP E 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE E 603 " --> pdb=" O LYS E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 623 removed outlier: 3.842A pdb=" N VAL E 623 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN E 645 " --> pdb=" O ALA E 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 161 Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU F 308 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 397 through 405 Processing helix chain 'F' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE F 558 " --> pdb=" O LEU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA F 592 " --> pdb=" O ASP F 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 603 " --> pdb=" O LYS F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 removed outlier: 3.842A pdb=" N VAL F 623 " --> pdb=" O ASP F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN F 645 " --> pdb=" O ALA F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 Processing helix chain 'G' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 161 Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL G 262 " --> pdb=" O VAL G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU G 308 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'G' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA G 592 " --> pdb=" O ASP G 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE G 603 " --> pdb=" O LYS G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL G 623 " --> pdb=" O ASP G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN G 645 " --> pdb=" O ALA G 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 Processing helix chain 'H' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 161 Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU H 308 " --> pdb=" O ASN H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 370 Processing helix chain 'H' and resid 397 through 405 Processing helix chain 'H' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE H 558 " --> pdb=" O LEU H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE H 565 " --> pdb=" O LEU H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA H 592 " --> pdb=" O ASP H 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE H 603 " --> pdb=" O LYS H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL H 623 " --> pdb=" O ASP H 620 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN H 645 " --> pdb=" O ALA H 641 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 161 Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL I 262 " --> pdb=" O VAL I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU I 308 " --> pdb=" O ASN I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 370 Processing helix chain 'I' and resid 397 through 405 Processing helix chain 'I' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA I 592 " --> pdb=" O ASP I 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 603 " --> pdb=" O LYS I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL I 623 " --> pdb=" O ASP I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN I 645 " --> pdb=" O ALA I 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 Processing helix chain 'J' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 161 Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY J 261 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL J 262 " --> pdb=" O VAL J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU J 308 " --> pdb=" O ASN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 370 Processing helix chain 'J' and resid 397 through 405 Processing helix chain 'J' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE J 558 " --> pdb=" O LEU J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE J 565 " --> pdb=" O LEU J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA J 592 " --> pdb=" O ASP J 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE J 603 " --> pdb=" O LYS J 599 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL J 623 " --> pdb=" O ASP J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN J 645 " --> pdb=" O ALA J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 Processing helix chain 'K' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 161 Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL K 262 " --> pdb=" O VAL K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU K 308 " --> pdb=" O ASN K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 370 Processing helix chain 'K' and resid 397 through 405 Processing helix chain 'K' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE K 558 " --> pdb=" O LEU K 554 " (cutoff:3.500A) Processing helix chain 'K' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE K 565 " --> pdb=" O LEU K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA K 592 " --> pdb=" O ASP K 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE K 603 " --> pdb=" O LYS K 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL K 623 " --> pdb=" O ASP K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN K 645 " --> pdb=" O ALA K 641 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 Processing helix chain 'L' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 161 Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY L 261 " --> pdb=" O GLU L 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL L 262 " --> pdb=" O VAL L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU L 308 " --> pdb=" O ASN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 370 Processing helix chain 'L' and resid 397 through 405 Processing helix chain 'L' and resid 553 through 558 removed outlier: 4.070A pdb=" N ILE L 558 " --> pdb=" O LEU L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE L 565 " --> pdb=" O LEU L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA L 592 " --> pdb=" O ASP L 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 603 " --> pdb=" O LYS L 599 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL L 623 " --> pdb=" O ASP L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN L 645 " --> pdb=" O ALA L 641 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 Processing helix chain 'M' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA M 126 " --> pdb=" O LEU M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 161 Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU M 232 " --> pdb=" O LEU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU M 308 " --> pdb=" O ASN M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 370 Processing helix chain 'M' and resid 397 through 405 Processing helix chain 'M' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE M 558 " --> pdb=" O LEU M 554 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE M 565 " --> pdb=" O LEU M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA M 592 " --> pdb=" O ASP M 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 603 " --> pdb=" O LYS M 599 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL M 623 " --> pdb=" O ASP M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 646 removed outlier: 3.639A pdb=" N GLN M 645 " --> pdb=" O ALA M 641 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 Processing helix chain 'N' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 161 Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL N 262 " --> pdb=" O VAL N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU N 308 " --> pdb=" O ASN N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 370 Processing helix chain 'N' and resid 397 through 405 Processing helix chain 'N' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE N 558 " --> pdb=" O LEU N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE N 565 " --> pdb=" O LEU N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA N 592 " --> pdb=" O ASP N 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE N 603 " --> pdb=" O LYS N 599 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL N 623 " --> pdb=" O ASP N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN N 645 " --> pdb=" O ALA N 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 Processing helix chain 'O' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 161 Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 264 removed outlier: 4.528A pdb=" N GLY O 261 " --> pdb=" O GLU O 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL O 262 " --> pdb=" O VAL O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU O 308 " --> pdb=" O ASN O 304 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 370 Processing helix chain 'O' and resid 397 through 405 Processing helix chain 'O' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE O 558 " --> pdb=" O LEU O 554 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE O 565 " --> pdb=" O LEU O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA O 592 " --> pdb=" O ASP O 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE O 603 " --> pdb=" O LYS O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL O 623 " --> pdb=" O ASP O 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN O 645 " --> pdb=" O ALA O 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 135 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE A 581 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 536 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU A 535 " --> pdb=" O MET B 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET B 443 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 537 " --> pdb=" O THR B 441 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 419 through 443 current: chain 'B' and resid 567 through 582 removed outlier: 6.595A pdb=" N ILE B 581 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 536 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU B 535 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET C 443 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 537 " --> pdb=" O THR C 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 581 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL C 536 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU C 535 " --> pdb=" O MET D 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET D 443 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 537 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 581 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL E 536 " --> pdb=" O ILE E 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU E 535 " --> pdb=" O MET F 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET F 443 " --> pdb=" O LEU E 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU E 537 " --> pdb=" O THR F 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 581 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL F 536 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU F 535 " --> pdb=" O MET G 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET G 443 " --> pdb=" O LEU F 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU F 537 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE G 581 " --> pdb=" O VAL G 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL G 536 " --> pdb=" O ILE G 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU G 535 " --> pdb=" O MET H 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET H 443 " --> pdb=" O LEU G 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU G 537 " --> pdb=" O THR H 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE H 581 " --> pdb=" O VAL H 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL H 536 " --> pdb=" O ILE H 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU H 535 " --> pdb=" O MET I 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET I 443 " --> pdb=" O LEU H 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU H 537 " --> pdb=" O THR I 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 581 " --> pdb=" O VAL I 536 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL I 536 " --> pdb=" O ILE I 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU I 535 " --> pdb=" O MET J 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET J 443 " --> pdb=" O LEU I 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU I 537 " --> pdb=" O THR J 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE J 581 " --> pdb=" O VAL J 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL J 536 " --> pdb=" O ILE J 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU J 535 " --> pdb=" O MET K 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET K 443 " --> pdb=" O LEU J 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU J 537 " --> pdb=" O THR K 441 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE K 581 " --> pdb=" O VAL K 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL K 536 " --> pdb=" O ILE K 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU K 535 " --> pdb=" O MET L 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET L 443 " --> pdb=" O LEU K 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU K 537 " --> pdb=" O THR L 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 581 " --> pdb=" O VAL L 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL L 536 " --> pdb=" O ILE L 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU L 535 " --> pdb=" O MET M 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET M 443 " --> pdb=" O LEU L 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU L 537 " --> pdb=" O THR M 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AA7, first strand: chain 'D' and resid 585 through 586 removed outlier: 6.594A pdb=" N ILE D 581 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D 536 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU D 535 " --> pdb=" O MET E 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET E 443 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 537 " --> pdb=" O THR E 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 585 through 586 Processing sheet with id=AA9, first strand: chain 'F' and resid 585 through 586 Processing sheet with id=AB1, first strand: chain 'G' and resid 585 through 586 Processing sheet with id=AB2, first strand: chain 'H' and resid 585 through 586 Processing sheet with id=AB3, first strand: chain 'I' and resid 585 through 586 Processing sheet with id=AB4, first strand: chain 'J' and resid 585 through 586 Processing sheet with id=AB5, first strand: chain 'K' and resid 585 through 586 Processing sheet with id=AB6, first strand: chain 'L' and resid 585 through 586 Processing sheet with id=AB7, first strand: chain 'M' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE M 581 " --> pdb=" O VAL M 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL M 536 " --> pdb=" O ILE M 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU M 535 " --> pdb=" O MET N 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET N 443 " --> pdb=" O LEU M 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU M 537 " --> pdb=" O THR N 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE N 581 " --> pdb=" O VAL N 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL N 536 " --> pdb=" O ILE N 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU N 535 " --> pdb=" O MET O 443 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N MET O 443 " --> pdb=" O LEU N 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU N 537 " --> pdb=" O THR O 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 585 through 586 removed outlier: 6.596A pdb=" N ILE O 581 " --> pdb=" O VAL O 536 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL O 536 " --> pdb=" O ILE O 581 " (cutoff:3.500A) removed outlier: 15.792A pdb=" N LEU O 535 " --> pdb=" O MET A 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET A 443 " --> pdb=" O LEU O 535 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU O 537 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.965A pdb=" N THR O 375 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR N 375 " --> pdb=" O THR O 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR M 375 " --> pdb=" O THR N 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR L 375 " --> pdb=" O THR M 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR K 375 " --> pdb=" O THR L 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR J 375 " --> pdb=" O THR K 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR I 375 " --> pdb=" O THR J 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR H 375 " --> pdb=" O THR I 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR G 375 " --> pdb=" O THR H 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR F 375 " --> pdb=" O THR G 392 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR E 375 " --> pdb=" O THR F 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 375 " --> pdb=" O THR E 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 375 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 375 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 375 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 448 through 455 removed outlier: 3.574A pdb=" N ASN A 499 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 504 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 518 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 455 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 453 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 499 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 504 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 518 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 455 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 453 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 499 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 504 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE C 518 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 455 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 453 " --> pdb=" O LYS C 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 499 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 504 " --> pdb=" O ARG D 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE D 518 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 455 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 453 " --> pdb=" O LYS D 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN E 499 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL E 504 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE E 518 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 455 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 453 " --> pdb=" O LYS E 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 499 " --> pdb=" O VAL F 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 504 " --> pdb=" O ARG F 521 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE F 518 " --> pdb=" O GLU G 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 455 " --> pdb=" O PHE F 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 453 " --> pdb=" O LYS F 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 499 " --> pdb=" O VAL G 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 504 " --> pdb=" O ARG G 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE G 518 " --> pdb=" O GLU H 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 455 " --> pdb=" O PHE G 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 453 " --> pdb=" O LYS G 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN H 499 " --> pdb=" O VAL H 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL H 504 " --> pdb=" O ARG H 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE H 518 " --> pdb=" O GLU I 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 455 " --> pdb=" O PHE H 518 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA I 453 " --> pdb=" O LYS H 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN I 499 " --> pdb=" O VAL I 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL I 504 " --> pdb=" O ARG I 521 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE I 518 " --> pdb=" O GLU J 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 455 " --> pdb=" O PHE I 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA J 453 " --> pdb=" O LYS I 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN J 499 " --> pdb=" O VAL J 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL J 504 " --> pdb=" O ARG J 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE J 518 " --> pdb=" O GLU K 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 455 " --> pdb=" O PHE J 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 453 " --> pdb=" O LYS J 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN K 499 " --> pdb=" O VAL K 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL K 504 " --> pdb=" O ARG K 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE K 518 " --> pdb=" O GLU L 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU L 455 " --> pdb=" O PHE K 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA L 453 " --> pdb=" O LYS K 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN L 499 " --> pdb=" O VAL L 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL L 504 " --> pdb=" O ARG L 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE L 518 " --> pdb=" O GLU M 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU M 455 " --> pdb=" O PHE L 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA M 453 " --> pdb=" O LYS L 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN M 499 " --> pdb=" O VAL M 487 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 504 " --> pdb=" O ARG M 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE M 518 " --> pdb=" O GLU N 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU N 455 " --> pdb=" O PHE M 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA N 453 " --> pdb=" O LYS M 520 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN N 499 " --> pdb=" O VAL N 487 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL N 504 " --> pdb=" O ARG N 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE N 518 " --> pdb=" O GLU O 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU O 455 " --> pdb=" O PHE N 518 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 453 " --> pdb=" O LYS N 520 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN O 499 " --> pdb=" O VAL O 487 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL O 504 " --> pdb=" O ARG O 521 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE O 518 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 455 " --> pdb=" O PHE O 518 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 453 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 135 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 166 through 171 Processing sheet with id=AC5, first strand: chain 'B' and resid 242 through 246 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP C 135 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 246 Processing sheet with id=AC9, first strand: chain 'D' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP D 135 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 166 through 171 Processing sheet with id=AD2, first strand: chain 'D' and resid 242 through 246 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP E 135 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 166 through 171 Processing sheet with id=AD5, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AD6, first strand: chain 'F' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP F 135 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 166 through 171 Processing sheet with id=AD8, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AD9, first strand: chain 'G' and resid 100 through 104 removed outlier: 3.672A pdb=" N ILE G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP G 135 " --> pdb=" O ILE G 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 166 through 171 Processing sheet with id=AE2, first strand: chain 'G' and resid 242 through 246 Processing sheet with id=AE3, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP H 135 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 166 through 171 Processing sheet with id=AE5, first strand: chain 'H' and resid 242 through 246 Processing sheet with id=AE6, first strand: chain 'I' and resid 100 through 104 removed outlier: 3.672A pdb=" N ILE I 139 " --> pdb=" O ASP I 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP I 135 " --> pdb=" O ILE I 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 166 through 171 Processing sheet with id=AE8, first strand: chain 'I' and resid 242 through 246 Processing sheet with id=AE9, first strand: chain 'J' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE J 139 " --> pdb=" O ASP J 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 135 " --> pdb=" O ILE J 139 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 166 through 171 Processing sheet with id=AF2, first strand: chain 'J' and resid 242 through 246 Processing sheet with id=AF3, first strand: chain 'K' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE K 139 " --> pdb=" O ASP K 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP K 135 " --> pdb=" O ILE K 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 166 through 171 Processing sheet with id=AF5, first strand: chain 'K' and resid 242 through 246 Processing sheet with id=AF6, first strand: chain 'L' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE L 139 " --> pdb=" O ASP L 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP L 135 " --> pdb=" O ILE L 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 166 through 171 Processing sheet with id=AF8, first strand: chain 'L' and resid 242 through 246 Processing sheet with id=AF9, first strand: chain 'M' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 135 " --> pdb=" O ILE M 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 166 through 171 Processing sheet with id=AG2, first strand: chain 'M' and resid 242 through 246 Processing sheet with id=AG3, first strand: chain 'N' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE N 139 " --> pdb=" O ASP N 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP N 135 " --> pdb=" O ILE N 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 166 through 171 Processing sheet with id=AG5, first strand: chain 'N' and resid 242 through 246 Processing sheet with id=AG6, first strand: chain 'O' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE O 139 " --> pdb=" O ASP O 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP O 135 " --> pdb=" O ILE O 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 166 through 171 Processing sheet with id=AG8, first strand: chain 'O' and resid 242 through 246 4161 hydrogen bonds defined for protein. 11673 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: 25.18 Time building geometry restraints manager: 17.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11167 1.32 - 1.44: 11258 1.44 - 1.56: 33975 1.56 - 1.68: 0 1.68 - 1.80: 390 Bond restraints: 56790 Sorted by residual: bond pdb=" N PRO M 457 " pdb=" CD PRO M 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.82e+01 bond pdb=" N PRO E 457 " pdb=" CD PRO E 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" N PRO J 457 " pdb=" CD PRO J 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" N PRO C 457 " pdb=" CD PRO C 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" N PRO B 457 " pdb=" CD PRO B 457 " ideal model delta sigma weight residual 1.473 1.547 -0.074 1.40e-02 5.10e+03 2.79e+01 ... (remaining 56785 not shown) Histogram of bond angle deviations from ideal: 91.07 - 101.66: 210 101.66 - 112.26: 30538 112.26 - 122.86: 39543 122.86 - 133.45: 6419 133.45 - 144.05: 45 Bond angle restraints: 76755 Sorted by residual: angle pdb=" C VAL E 507 " pdb=" CA VAL E 507 " pdb=" CB VAL E 507 " ideal model delta sigma weight residual 110.28 91.07 19.21 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL B 507 " pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta sigma weight residual 110.28 91.07 19.21 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL C 507 " pdb=" CA VAL C 507 " pdb=" CB VAL C 507 " ideal model delta sigma weight residual 110.28 91.07 19.21 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL I 507 " pdb=" CA VAL I 507 " pdb=" CB VAL I 507 " ideal model delta sigma weight residual 110.28 91.08 19.20 1.58e+00 4.01e-01 1.48e+02 angle pdb=" C VAL M 507 " pdb=" CA VAL M 507 " pdb=" CB VAL M 507 " ideal model delta sigma weight residual 110.28 91.08 19.20 1.58e+00 4.01e-01 1.48e+02 ... (remaining 76750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 32881 16.11 - 32.23: 1769 32.23 - 48.34: 360 48.34 - 64.46: 90 64.46 - 80.57: 90 Dihedral angle restraints: 35190 sinusoidal: 14010 harmonic: 21180 Sorted by residual: dihedral pdb=" C VAL B 507 " pdb=" N VAL B 507 " pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta harmonic sigma weight residual -122.00 -101.30 -20.70 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" C VAL C 507 " pdb=" N VAL C 507 " pdb=" CA VAL C 507 " pdb=" CB VAL C 507 " ideal model delta harmonic sigma weight residual -122.00 -101.31 -20.69 0 2.50e+00 1.60e-01 6.85e+01 dihedral pdb=" C VAL E 507 " pdb=" N VAL E 507 " pdb=" CA VAL E 507 " pdb=" CB VAL E 507 " ideal model delta harmonic sigma weight residual -122.00 -101.33 -20.67 0 2.50e+00 1.60e-01 6.84e+01 ... (remaining 35187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 7586 0.081 - 0.162: 1588 0.162 - 0.243: 156 0.243 - 0.323: 30 0.323 - 0.404: 15 Chirality restraints: 9375 Sorted by residual: chirality pdb=" CA VAL B 507 " pdb=" N VAL B 507 " pdb=" C VAL B 507 " pdb=" CB VAL B 507 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA VAL H 507 " pdb=" N VAL H 507 " pdb=" C VAL H 507 " pdb=" CB VAL H 507 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA VAL C 507 " pdb=" N VAL C 507 " pdb=" C VAL C 507 " pdb=" CB VAL C 507 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 9372 not shown) Planarity restraints: 9975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO N 438 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO N 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO N 438 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO F 438 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO F 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO F 438 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO H 438 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO H 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO H 438 " 0.071 5.00e-02 4.00e+02 ... (remaining 9972 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 285 2.18 - 2.86: 20069 2.86 - 3.54: 77408 3.54 - 4.22: 126898 4.22 - 4.90: 224169 Nonbonded interactions: 448829 Sorted by model distance: nonbonded pdb=" CE1 PHE J 518 " pdb=" OE2 GLU K 455 " model vdw 1.501 3.340 nonbonded pdb=" CE1 PHE K 518 " pdb=" OE2 GLU L 455 " model vdw 1.502 3.340 nonbonded pdb=" OE2 GLU A 455 " pdb=" CE1 PHE O 518 " model vdw 1.502 3.340 nonbonded pdb=" CE1 PHE A 518 " pdb=" OE2 GLU B 455 " model vdw 1.502 3.340 nonbonded pdb=" CE1 PHE C 518 " pdb=" OE2 GLU D 455 " model vdw 1.502 3.340 ... (remaining 448824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.040 Extract box with map and model: 12.710 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 116.550 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 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 : 0.009 0.092 56790 Z= 0.559 Angle : 1.221 19.214 76755 Z= 0.697 Chirality : 0.066 0.404 9375 Planarity : 0.007 0.139 9975 Dihedral : 11.966 80.571 21420 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 38.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.38 % Favored : 95.41 % Rotamer: Outliers : 2.89 % Allowed : 5.78 % Favored : 91.33 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.09), residues: 7215 helix: -2.39 (0.10), residues: 1860 sheet: -1.12 (0.08), residues: 3090 loop : -0.89 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 341 HIS 0.004 0.001 HIS F 288 PHE 0.015 0.002 PHE K 580 TYR 0.035 0.003 TYR I 134 ARG 0.010 0.002 ARG I 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1980 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1800 time to evaluate : 5.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8516 (mmm) cc_final: 0.7860 (mmm) REVERT: A 490 ILE cc_start: 0.7732 (mt) cc_final: 0.7489 (mt) REVERT: A 496 VAL cc_start: 0.8290 (t) cc_final: 0.8067 (t) REVERT: A 503 GLU cc_start: 0.8497 (tt0) cc_final: 0.8202 (tm-30) REVERT: A 591 THR cc_start: 0.7156 (m) cc_final: 0.6741 (p) REVERT: A 607 GLN cc_start: 0.8276 (mt0) cc_final: 0.7470 (mt0) REVERT: A 643 ILE cc_start: 0.8757 (tp) cc_final: 0.8083 (tp) REVERT: B 180 MET cc_start: 0.8596 (mmm) cc_final: 0.7853 (mmm) REVERT: B 296 LEU cc_start: 0.8291 (mt) cc_final: 0.7914 (mt) REVERT: B 397 TYR cc_start: 0.8462 (m-80) cc_final: 0.8141 (m-80) REVERT: B 443 MET cc_start: 0.8122 (tpp) cc_final: 0.7904 (tpp) REVERT: B 591 THR cc_start: 0.7133 (m) cc_final: 0.6698 (p) REVERT: B 607 GLN cc_start: 0.8427 (mt0) cc_final: 0.7861 (mm110) REVERT: B 643 ILE cc_start: 0.8607 (tp) cc_final: 0.8081 (tp) REVERT: C 180 MET cc_start: 0.8484 (mmm) cc_final: 0.7553 (mmm) REVERT: C 296 LEU cc_start: 0.8279 (mt) cc_final: 0.7800 (mt) REVERT: C 302 ILE cc_start: 0.7231 (mt) cc_final: 0.6978 (mm) REVERT: C 363 MET cc_start: 0.8868 (mtm) cc_final: 0.8369 (mtm) REVERT: C 607 GLN cc_start: 0.8449 (mt0) cc_final: 0.8134 (mm-40) REVERT: C 643 ILE cc_start: 0.8677 (tp) cc_final: 0.7998 (tp) REVERT: D 180 MET cc_start: 0.8533 (mmm) cc_final: 0.7768 (mmm) REVERT: D 296 LEU cc_start: 0.8299 (mt) cc_final: 0.7863 (mt) REVERT: D 591 THR cc_start: 0.7246 (m) cc_final: 0.7011 (m) REVERT: D 607 GLN cc_start: 0.8230 (mt0) cc_final: 0.7715 (mm110) REVERT: D 643 ILE cc_start: 0.8539 (tp) cc_final: 0.7820 (tp) REVERT: E 180 MET cc_start: 0.8536 (mmm) cc_final: 0.7899 (mmm) REVERT: E 322 ILE cc_start: 0.6898 (mm) cc_final: 0.6669 (mm) REVERT: E 591 THR cc_start: 0.7349 (m) cc_final: 0.6843 (p) REVERT: E 607 GLN cc_start: 0.8340 (mt0) cc_final: 0.7575 (mt0) REVERT: F 180 MET cc_start: 0.8524 (mmm) cc_final: 0.7902 (mmm) REVERT: F 302 ILE cc_start: 0.7357 (mt) cc_final: 0.7090 (mm) REVERT: F 363 MET cc_start: 0.8569 (mtm) cc_final: 0.8253 (mtm) REVERT: F 591 THR cc_start: 0.7053 (m) cc_final: 0.6718 (p) REVERT: F 600 TYR cc_start: 0.6797 (t80) cc_final: 0.6359 (t80) REVERT: F 607 GLN cc_start: 0.8332 (mt0) cc_final: 0.7780 (mm-40) REVERT: F 643 ILE cc_start: 0.8698 (tp) cc_final: 0.7880 (tp) REVERT: G 180 MET cc_start: 0.8519 (mmm) cc_final: 0.7741 (mmm) REVERT: G 363 MET cc_start: 0.8598 (mtm) cc_final: 0.8157 (mtm) REVERT: G 420 THR cc_start: 0.8017 (p) cc_final: 0.7767 (p) REVERT: G 607 GLN cc_start: 0.8306 (mt0) cc_final: 0.7849 (mm-40) REVERT: G 643 ILE cc_start: 0.8646 (tp) cc_final: 0.8060 (tp) REVERT: H 180 MET cc_start: 0.8438 (mmm) cc_final: 0.7813 (mmm) REVERT: H 296 LEU cc_start: 0.8383 (mt) cc_final: 0.8011 (mt) REVERT: H 496 VAL cc_start: 0.8462 (t) cc_final: 0.8249 (t) REVERT: H 591 THR cc_start: 0.7137 (m) cc_final: 0.6809 (m) REVERT: H 607 GLN cc_start: 0.8426 (mt0) cc_final: 0.7960 (mm-40) REVERT: H 643 ILE cc_start: 0.8525 (tp) cc_final: 0.7849 (tp) REVERT: I 180 MET cc_start: 0.8406 (mmm) cc_final: 0.7517 (mmm) REVERT: I 296 LEU cc_start: 0.8067 (mt) cc_final: 0.7568 (mt) REVERT: I 496 VAL cc_start: 0.8436 (t) cc_final: 0.8209 (t) REVERT: I 607 GLN cc_start: 0.8252 (mt0) cc_final: 0.7736 (mm110) REVERT: I 643 ILE cc_start: 0.8715 (tp) cc_final: 0.7925 (tp) REVERT: J 180 MET cc_start: 0.8620 (mmm) cc_final: 0.7999 (mmm) REVERT: J 302 ILE cc_start: 0.7700 (mt) cc_final: 0.7415 (mm) REVERT: J 363 MET cc_start: 0.8630 (mtm) cc_final: 0.8105 (mtm) REVERT: J 420 THR cc_start: 0.8069 (p) cc_final: 0.7861 (p) REVERT: J 591 THR cc_start: 0.7345 (m) cc_final: 0.7038 (p) REVERT: J 607 GLN cc_start: 0.8365 (mt0) cc_final: 0.7796 (mm-40) REVERT: K 180 MET cc_start: 0.8592 (mmm) cc_final: 0.7725 (mmm) REVERT: K 296 LEU cc_start: 0.8287 (mt) cc_final: 0.7910 (mt) REVERT: K 302 ILE cc_start: 0.7414 (mt) cc_final: 0.7130 (mm) REVERT: K 496 VAL cc_start: 0.8173 (t) cc_final: 0.7883 (t) REVERT: K 503 GLU cc_start: 0.8565 (tt0) cc_final: 0.8290 (tm-30) REVERT: K 600 TYR cc_start: 0.6997 (t80) cc_final: 0.6791 (t80) REVERT: K 607 GLN cc_start: 0.8528 (mt0) cc_final: 0.7909 (mm-40) REVERT: K 643 ILE cc_start: 0.8737 (tp) cc_final: 0.8065 (tp) REVERT: L 180 MET cc_start: 0.8614 (mmm) cc_final: 0.8040 (mmm) REVERT: L 296 LEU cc_start: 0.8251 (mt) cc_final: 0.7832 (mt) REVERT: L 322 ILE cc_start: 0.7020 (mm) cc_final: 0.6736 (mm) REVERT: L 363 MET cc_start: 0.8642 (mtm) cc_final: 0.8221 (mtm) REVERT: L 397 TYR cc_start: 0.8757 (m-80) cc_final: 0.8521 (m-10) REVERT: L 476 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6866 (t0) REVERT: L 607 GLN cc_start: 0.8342 (mt0) cc_final: 0.7859 (mm-40) REVERT: L 643 ILE cc_start: 0.8643 (tp) cc_final: 0.7779 (tp) REVERT: M 180 MET cc_start: 0.8567 (mmm) cc_final: 0.7705 (mmm) REVERT: M 591 THR cc_start: 0.6794 (m) cc_final: 0.6579 (m) REVERT: M 607 GLN cc_start: 0.8411 (mt0) cc_final: 0.7840 (mm-40) REVERT: M 643 ILE cc_start: 0.8639 (tp) cc_final: 0.7955 (tp) REVERT: N 180 MET cc_start: 0.8542 (mmm) cc_final: 0.7941 (mmm) REVERT: N 302 ILE cc_start: 0.7452 (mt) cc_final: 0.6607 (mm) REVERT: N 591 THR cc_start: 0.7140 (m) cc_final: 0.6739 (p) REVERT: N 607 GLN cc_start: 0.8436 (mt0) cc_final: 0.8123 (mm110) REVERT: N 643 ILE cc_start: 0.8636 (tp) cc_final: 0.7787 (tp) REVERT: O 180 MET cc_start: 0.8577 (mmm) cc_final: 0.7954 (mmm) REVERT: O 296 LEU cc_start: 0.8256 (mt) cc_final: 0.7834 (mt) REVERT: O 302 ILE cc_start: 0.7180 (mt) cc_final: 0.6941 (mm) REVERT: O 413 SER cc_start: 0.8927 (m) cc_final: 0.8720 (p) REVERT: O 591 THR cc_start: 0.6713 (m) cc_final: 0.6494 (m) REVERT: O 607 GLN cc_start: 0.8500 (mt0) cc_final: 0.7889 (mm-40) REVERT: O 643 ILE cc_start: 0.8732 (tp) cc_final: 0.8065 (tp) outliers start: 180 outliers final: 67 residues processed: 1965 average time/residue: 0.5442 time to fit residues: 1777.8976 Evaluate side-chains 1075 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1007 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 7.9990 chunk 557 optimal weight: 0.6980 chunk 309 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 chunk 297 optimal weight: 20.0000 chunk 576 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 667 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 340 GLN A 361 ASN A 424 ASN A 502 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN B 288 HIS B 424 ASN B 502 GLN B 506 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 288 HIS ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 424 ASN C 502 GLN C 640 GLN D 288 HIS D 340 GLN D 424 ASN D 502 GLN D 640 GLN E 288 HIS E 336 ASN E 340 GLN E 361 ASN E 424 ASN E 502 GLN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 288 HIS F 340 GLN F 424 ASN F 502 GLN ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN G 288 HIS G 340 GLN G 354 ASN G 361 ASN G 424 ASN G 502 GLN G 640 GLN H 288 HIS H 340 GLN H 424 ASN H 502 GLN H 640 GLN ** I 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 HIS I 340 GLN I 361 ASN I 424 ASN I 502 GLN ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 640 GLN J 288 HIS J 340 GLN J 424 ASN J 502 GLN ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN K 288 HIS K 424 ASN K 502 GLN ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 640 GLN L 288 HIS L 340 GLN L 424 ASN L 502 GLN L 640 GLN M 288 HIS M 424 ASN M 502 GLN M 571 GLN M 640 GLN N 288 HIS N 340 GLN N 361 ASN N 424 ASN N 502 GLN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 640 GLN O 288 HIS O 340 GLN O 424 ASN O 502 GLN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 640 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 56790 Z= 0.285 Angle : 0.802 10.943 76755 Z= 0.419 Chirality : 0.051 0.202 9375 Planarity : 0.006 0.070 9975 Dihedral : 6.012 26.591 7800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.53 % Allowed : 4.18 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.09), residues: 7215 helix: -0.78 (0.10), residues: 2115 sheet: -0.57 (0.08), residues: 3150 loop : -0.57 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 341 HIS 0.004 0.001 HIS N 635 PHE 0.020 0.002 PHE M 450 TYR 0.017 0.003 TYR J 134 ARG 0.009 0.001 ARG L 521 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1233 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8275 (mmm) cc_final: 0.7924 (mmm) REVERT: A 236 MET cc_start: 0.6622 (mmp) cc_final: 0.6060 (mmt) REVERT: A 254 ASP cc_start: 0.8775 (m-30) cc_final: 0.8550 (t0) REVERT: A 296 LEU cc_start: 0.8708 (mt) cc_final: 0.8230 (mt) REVERT: A 302 ILE cc_start: 0.7948 (mm) cc_final: 0.7579 (mm) REVERT: A 306 MET cc_start: 0.8722 (mtm) cc_final: 0.8435 (mtt) REVERT: A 363 MET cc_start: 0.9250 (ptm) cc_final: 0.9013 (ptm) REVERT: A 503 GLU cc_start: 0.8275 (tt0) cc_final: 0.8074 (tm-30) REVERT: A 586 ILE cc_start: 0.8953 (mm) cc_final: 0.8751 (mm) REVERT: A 642 PHE cc_start: 0.8242 (t80) cc_final: 0.7641 (t80) REVERT: B 180 MET cc_start: 0.8530 (mmm) cc_final: 0.8076 (mmm) REVERT: B 302 ILE cc_start: 0.8125 (mm) cc_final: 0.7349 (mp) REVERT: B 306 MET cc_start: 0.8811 (mtm) cc_final: 0.8414 (mtt) REVERT: B 333 ASP cc_start: 0.8203 (p0) cc_final: 0.7696 (p0) REVERT: B 363 MET cc_start: 0.8828 (mtp) cc_final: 0.8529 (mtm) REVERT: B 607 GLN cc_start: 0.8153 (mt0) cc_final: 0.7805 (mt0) REVERT: B 624 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8140 (Cg_exo) REVERT: B 642 PHE cc_start: 0.8307 (t80) cc_final: 0.7394 (t80) REVERT: C 180 MET cc_start: 0.8353 (mmm) cc_final: 0.8120 (mmm) REVERT: C 284 MET cc_start: 0.8629 (mpp) cc_final: 0.8264 (mpp) REVERT: C 306 MET cc_start: 0.9111 (mpp) cc_final: 0.8460 (mmp) REVERT: C 333 ASP cc_start: 0.8067 (p0) cc_final: 0.7593 (p0) REVERT: C 443 MET cc_start: 0.8661 (tpp) cc_final: 0.8191 (tpp) REVERT: C 505 SER cc_start: 0.8911 (t) cc_final: 0.8688 (t) REVERT: C 602 TYR cc_start: 0.7277 (t80) cc_final: 0.6998 (t80) REVERT: C 607 GLN cc_start: 0.8142 (mt0) cc_final: 0.7624 (mt0) REVERT: C 609 PHE cc_start: 0.8011 (t80) cc_final: 0.7216 (t80) REVERT: C 643 ILE cc_start: 0.8639 (tp) cc_final: 0.8423 (tt) REVERT: D 180 MET cc_start: 0.8421 (mmm) cc_final: 0.8090 (mmm) REVERT: D 236 MET cc_start: 0.7405 (mmp) cc_final: 0.6995 (mmt) REVERT: D 254 ASP cc_start: 0.8683 (m-30) cc_final: 0.8412 (t0) REVERT: D 284 MET cc_start: 0.8636 (mpp) cc_final: 0.8370 (mpp) REVERT: D 329 MET cc_start: 0.8219 (mtm) cc_final: 0.7910 (mtm) REVERT: D 501 GLU cc_start: 0.8442 (mp0) cc_final: 0.8235 (mp0) REVERT: D 607 GLN cc_start: 0.8083 (mt0) cc_final: 0.7689 (mt0) REVERT: D 643 ILE cc_start: 0.8415 (tp) cc_final: 0.7957 (tp) REVERT: E 180 MET cc_start: 0.8387 (mmm) cc_final: 0.8060 (mmm) REVERT: E 236 MET cc_start: 0.6700 (mmp) cc_final: 0.5534 (mmt) REVERT: E 254 ASP cc_start: 0.8747 (m-30) cc_final: 0.8531 (t0) REVERT: E 284 MET cc_start: 0.8264 (mpp) cc_final: 0.7917 (mpp) REVERT: E 302 ILE cc_start: 0.8459 (mm) cc_final: 0.8126 (mp) REVERT: E 306 MET cc_start: 0.8885 (mtm) cc_final: 0.8623 (mtp) REVERT: E 336 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7948 (m110) REVERT: E 480 VAL cc_start: 0.7705 (m) cc_final: 0.7416 (p) REVERT: E 505 SER cc_start: 0.8882 (t) cc_final: 0.8483 (t) REVERT: E 607 GLN cc_start: 0.8370 (mt0) cc_final: 0.7838 (mm-40) REVERT: F 180 MET cc_start: 0.8411 (mmm) cc_final: 0.8111 (mmm) REVERT: F 211 ASN cc_start: 0.8136 (t0) cc_final: 0.7789 (t0) REVERT: F 236 MET cc_start: 0.7363 (mmp) cc_final: 0.7161 (mmt) REVERT: F 254 ASP cc_start: 0.8874 (m-30) cc_final: 0.8645 (t0) REVERT: F 284 MET cc_start: 0.8371 (mpp) cc_final: 0.7950 (mpp) REVERT: F 296 LEU cc_start: 0.8777 (mt) cc_final: 0.8205 (mt) REVERT: F 363 MET cc_start: 0.9007 (mtm) cc_final: 0.8330 (mtm) REVERT: F 501 GLU cc_start: 0.8389 (mp0) cc_final: 0.8177 (mp0) REVERT: F 607 GLN cc_start: 0.8319 (mt0) cc_final: 0.7611 (mt0) REVERT: F 643 ILE cc_start: 0.8687 (tp) cc_final: 0.8410 (tt) REVERT: G 180 MET cc_start: 0.8283 (mmm) cc_final: 0.7814 (mmm) REVERT: G 284 MET cc_start: 0.8052 (mpp) cc_final: 0.7728 (mpp) REVERT: G 443 MET cc_start: 0.8834 (tpp) cc_final: 0.8267 (tpp) REVERT: G 607 GLN cc_start: 0.8238 (mt0) cc_final: 0.7760 (mt0) REVERT: G 642 PHE cc_start: 0.8240 (t80) cc_final: 0.7808 (t80) REVERT: H 180 MET cc_start: 0.8273 (mmm) cc_final: 0.7899 (mmm) REVERT: H 236 MET cc_start: 0.7274 (mmp) cc_final: 0.6656 (mmt) REVERT: H 254 ASP cc_start: 0.8668 (m-30) cc_final: 0.8319 (t0) REVERT: H 284 MET cc_start: 0.8460 (mpp) cc_final: 0.8201 (mpp) REVERT: H 333 ASP cc_start: 0.8194 (p0) cc_final: 0.7710 (p0) REVERT: H 443 MET cc_start: 0.8850 (tpp) cc_final: 0.8434 (tpp) REVERT: H 607 GLN cc_start: 0.8381 (mt0) cc_final: 0.7765 (mt0) REVERT: H 642 PHE cc_start: 0.8384 (t80) cc_final: 0.7840 (t80) REVERT: I 180 MET cc_start: 0.8152 (mmm) cc_final: 0.7832 (mmm) REVERT: I 254 ASP cc_start: 0.8887 (m-30) cc_final: 0.8400 (t0) REVERT: I 284 MET cc_start: 0.8645 (mpp) cc_final: 0.8359 (mpp) REVERT: I 602 TYR cc_start: 0.7864 (t80) cc_final: 0.7353 (t80) REVERT: I 607 GLN cc_start: 0.8156 (mt0) cc_final: 0.7676 (mt0) REVERT: I 609 PHE cc_start: 0.8115 (t80) cc_final: 0.7707 (t80) REVERT: I 642 PHE cc_start: 0.8178 (t80) cc_final: 0.7595 (t80) REVERT: J 180 MET cc_start: 0.8492 (mmm) cc_final: 0.8124 (mmm) REVERT: J 284 MET cc_start: 0.8159 (mpp) cc_final: 0.7763 (mpp) REVERT: J 296 LEU cc_start: 0.8702 (mt) cc_final: 0.8229 (mt) REVERT: J 363 MET cc_start: 0.8924 (mtm) cc_final: 0.8152 (mtm) REVERT: J 447 GLU cc_start: 0.9069 (pm20) cc_final: 0.8689 (pp20) REVERT: J 607 GLN cc_start: 0.8359 (mt0) cc_final: 0.7489 (mt0) REVERT: J 642 PHE cc_start: 0.8314 (t80) cc_final: 0.7797 (t80) REVERT: K 180 MET cc_start: 0.8247 (mmm) cc_final: 0.7801 (mmm) REVERT: K 284 MET cc_start: 0.8338 (mpp) cc_final: 0.7888 (mpp) REVERT: K 333 ASP cc_start: 0.8181 (p0) cc_final: 0.7761 (p0) REVERT: K 363 MET cc_start: 0.9231 (ptm) cc_final: 0.8628 (ppp) REVERT: K 443 MET cc_start: 0.8872 (tpp) cc_final: 0.8230 (mmm) REVERT: K 480 VAL cc_start: 0.7942 (m) cc_final: 0.7721 (m) REVERT: K 503 GLU cc_start: 0.8194 (tt0) cc_final: 0.7924 (tm-30) REVERT: K 607 GLN cc_start: 0.8257 (mt0) cc_final: 0.7896 (mt0) REVERT: K 642 PHE cc_start: 0.8219 (t80) cc_final: 0.7554 (t80) REVERT: L 180 MET cc_start: 0.8486 (mmm) cc_final: 0.8046 (mmm) REVERT: L 284 MET cc_start: 0.8388 (mpp) cc_final: 0.8028 (mpp) REVERT: L 303 MET cc_start: 0.6473 (ttt) cc_final: 0.6269 (ttt) REVERT: L 359 ILE cc_start: 0.8496 (tt) cc_final: 0.8287 (tt) REVERT: L 363 MET cc_start: 0.8855 (mtm) cc_final: 0.8537 (mtm) REVERT: L 397 TYR cc_start: 0.8692 (m-80) cc_final: 0.8455 (m-10) REVERT: L 561 LEU cc_start: 0.9045 (pp) cc_final: 0.8843 (pp) REVERT: L 603 ILE cc_start: 0.8996 (mt) cc_final: 0.8796 (mm) REVERT: L 606 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8685 (tm-30) REVERT: L 607 GLN cc_start: 0.8457 (mt0) cc_final: 0.7844 (mt0) REVERT: M 180 MET cc_start: 0.8312 (mmm) cc_final: 0.8034 (mmm) REVERT: M 296 LEU cc_start: 0.8926 (mt) cc_final: 0.8253 (mt) REVERT: M 363 MET cc_start: 0.9219 (ptm) cc_final: 0.8624 (ptm) REVERT: M 505 SER cc_start: 0.8935 (t) cc_final: 0.8677 (p) REVERT: M 565 PHE cc_start: 0.8513 (m-80) cc_final: 0.8260 (m-10) REVERT: M 607 GLN cc_start: 0.8423 (mt0) cc_final: 0.7867 (mt0) REVERT: M 609 PHE cc_start: 0.8202 (t80) cc_final: 0.7406 (t80) REVERT: N 180 MET cc_start: 0.8378 (mmm) cc_final: 0.8052 (mmm) REVERT: N 242 ASN cc_start: 0.6051 (p0) cc_final: 0.5674 (p0) REVERT: N 363 MET cc_start: 0.8895 (ptp) cc_final: 0.8644 (ptp) REVERT: N 443 MET cc_start: 0.9053 (tpp) cc_final: 0.8701 (tpp) REVERT: N 607 GLN cc_start: 0.8392 (mt0) cc_final: 0.7994 (mt0) REVERT: N 642 PHE cc_start: 0.8200 (t80) cc_final: 0.7612 (t80) REVERT: O 180 MET cc_start: 0.8357 (mmm) cc_final: 0.8086 (mmm) REVERT: O 254 ASP cc_start: 0.8716 (m-30) cc_final: 0.8358 (t0) REVERT: O 284 MET cc_start: 0.8617 (mpp) cc_final: 0.8350 (mpp) REVERT: O 607 GLN cc_start: 0.8222 (mt0) cc_final: 0.7606 (mt0) REVERT: O 624 PRO cc_start: 0.8292 (Cg_endo) cc_final: 0.8006 (Cg_exo) REVERT: O 642 PHE cc_start: 0.8345 (t80) cc_final: 0.7792 (t80) outliers start: 33 outliers final: 3 residues processed: 1265 average time/residue: 0.4899 time to fit residues: 1073.7607 Evaluate side-chains 842 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 838 time to evaluate : 4.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 555 optimal weight: 0.6980 chunk 454 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 668 optimal weight: 5.9990 chunk 722 optimal weight: 0.9980 chunk 595 optimal weight: 9.9990 chunk 663 optimal weight: 0.0970 chunk 227 optimal weight: 1.9990 chunk 536 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 361 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN D 361 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 GLN E 300 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN G 300 GLN ** G 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN H 354 ASN ** H 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 ASN I 242 ASN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 354 ASN K 361 ASN ** K 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 ASN ** L 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 GLN M 361 ASN ** M 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 354 ASN O 361 ASN ** O 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 56790 Z= 0.220 Angle : 0.699 10.810 76755 Z= 0.366 Chirality : 0.051 0.176 9375 Planarity : 0.005 0.058 9975 Dihedral : 5.305 22.132 7800 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.31 % Allowed : 4.16 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.09), residues: 7215 helix: 0.15 (0.11), residues: 2130 sheet: -0.23 (0.08), residues: 3090 loop : -0.52 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 419 HIS 0.004 0.001 HIS O 288 PHE 0.018 0.002 PHE O 642 TYR 0.022 0.002 TYR I 352 ARG 0.006 0.000 ARG F 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1047 time to evaluate : 5.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8309 (mmm) cc_final: 0.7974 (mmm) REVERT: A 302 ILE cc_start: 0.8275 (mm) cc_final: 0.7590 (mp) REVERT: A 306 MET cc_start: 0.9040 (mtm) cc_final: 0.8671 (mtt) REVERT: A 443 MET cc_start: 0.9115 (tpp) cc_final: 0.8379 (mmm) REVERT: A 501 GLU cc_start: 0.8604 (pm20) cc_final: 0.8352 (pm20) REVERT: B 180 MET cc_start: 0.8545 (mmm) cc_final: 0.8185 (mmm) REVERT: B 284 MET cc_start: 0.8553 (mpp) cc_final: 0.8297 (mpp) REVERT: B 302 ILE cc_start: 0.8211 (mm) cc_final: 0.7736 (mp) REVERT: B 306 MET cc_start: 0.8863 (mtm) cc_final: 0.8584 (mmt) REVERT: B 333 ASP cc_start: 0.8173 (p0) cc_final: 0.7638 (p0) REVERT: B 443 MET cc_start: 0.8825 (tpp) cc_final: 0.8406 (mmm) REVERT: B 607 GLN cc_start: 0.8511 (mt0) cc_final: 0.8005 (mt0) REVERT: C 211 ASN cc_start: 0.8049 (t0) cc_final: 0.7804 (t0) REVERT: C 284 MET cc_start: 0.8547 (mpp) cc_final: 0.8059 (mpp) REVERT: C 306 MET cc_start: 0.9081 (mpp) cc_final: 0.8503 (mmm) REVERT: C 333 ASP cc_start: 0.8104 (p0) cc_final: 0.7808 (p0) REVERT: C 363 MET cc_start: 0.9182 (ptp) cc_final: 0.8856 (ptp) REVERT: C 443 MET cc_start: 0.8880 (tpp) cc_final: 0.8269 (tmm) REVERT: C 607 GLN cc_start: 0.8260 (mt0) cc_final: 0.7644 (mt0) REVERT: C 642 PHE cc_start: 0.8344 (t80) cc_final: 0.7544 (t80) REVERT: D 180 MET cc_start: 0.8481 (mmm) cc_final: 0.8089 (mmm) REVERT: D 254 ASP cc_start: 0.8701 (m-30) cc_final: 0.8361 (t0) REVERT: D 284 MET cc_start: 0.8686 (mpp) cc_final: 0.8129 (mpp) REVERT: D 607 GLN cc_start: 0.8680 (mt0) cc_final: 0.7968 (mt0) REVERT: D 642 PHE cc_start: 0.8040 (t80) cc_final: 0.7192 (t80) REVERT: E 180 MET cc_start: 0.8457 (mmm) cc_final: 0.8077 (mmm) REVERT: E 254 ASP cc_start: 0.8728 (m-30) cc_final: 0.8358 (t0) REVERT: E 284 MET cc_start: 0.8348 (mpp) cc_final: 0.7914 (mpp) REVERT: E 607 GLN cc_start: 0.8421 (mt0) cc_final: 0.7792 (mt0) REVERT: F 180 MET cc_start: 0.8478 (mmm) cc_final: 0.8165 (mmm) REVERT: F 211 ASN cc_start: 0.8397 (t0) cc_final: 0.7591 (t0) REVERT: F 254 ASP cc_start: 0.8741 (m-30) cc_final: 0.8494 (t0) REVERT: F 363 MET cc_start: 0.9065 (mtm) cc_final: 0.8850 (mtm) REVERT: F 607 GLN cc_start: 0.8534 (mt0) cc_final: 0.7910 (mt0) REVERT: F 642 PHE cc_start: 0.8594 (t80) cc_final: 0.7971 (t80) REVERT: G 180 MET cc_start: 0.8225 (mmm) cc_final: 0.7894 (mmm) REVERT: G 211 ASN cc_start: 0.8100 (t0) cc_final: 0.7611 (t0) REVERT: G 284 MET cc_start: 0.8160 (mpp) cc_final: 0.7700 (mpp) REVERT: G 333 ASP cc_start: 0.8299 (p0) cc_final: 0.7980 (p0) REVERT: G 352 TYR cc_start: 0.8026 (m-10) cc_final: 0.7722 (m-10) REVERT: G 363 MET cc_start: 0.9186 (ptp) cc_final: 0.8796 (ptp) REVERT: G 607 GLN cc_start: 0.8173 (mt0) cc_final: 0.7817 (mt0) REVERT: H 180 MET cc_start: 0.8392 (mmm) cc_final: 0.8015 (mmm) REVERT: H 284 MET cc_start: 0.8541 (mpp) cc_final: 0.8282 (mpp) REVERT: H 352 TYR cc_start: 0.8105 (m-10) cc_final: 0.7793 (m-10) REVERT: H 602 TYR cc_start: 0.8255 (t80) cc_final: 0.7928 (t80) REVERT: H 607 GLN cc_start: 0.8594 (mt0) cc_final: 0.8069 (mt0) REVERT: I 180 MET cc_start: 0.8444 (mmm) cc_final: 0.8233 (mmm) REVERT: I 254 ASP cc_start: 0.8906 (m-30) cc_final: 0.8366 (t0) REVERT: I 284 MET cc_start: 0.8555 (mpp) cc_final: 0.8179 (mpp) REVERT: I 333 ASP cc_start: 0.7992 (p0) cc_final: 0.7694 (p0) REVERT: I 363 MET cc_start: 0.9076 (mtm) cc_final: 0.8656 (mtm) REVERT: I 443 MET cc_start: 0.8600 (tpp) cc_final: 0.8397 (mmm) REVERT: I 602 TYR cc_start: 0.8362 (t80) cc_final: 0.7758 (t80) REVERT: I 607 GLN cc_start: 0.8449 (mt0) cc_final: 0.8000 (mt0) REVERT: J 180 MET cc_start: 0.8408 (mmm) cc_final: 0.8102 (mmm) REVERT: J 284 MET cc_start: 0.8097 (mpp) cc_final: 0.7676 (mpp) REVERT: J 321 LEU cc_start: 0.8766 (tp) cc_final: 0.8473 (tp) REVERT: J 443 MET cc_start: 0.9216 (tpp) cc_final: 0.8436 (tpp) REVERT: J 607 GLN cc_start: 0.8437 (mt0) cc_final: 0.7886 (mt0) REVERT: K 180 MET cc_start: 0.8199 (mmm) cc_final: 0.7851 (mmm) REVERT: K 284 MET cc_start: 0.8331 (mpp) cc_final: 0.7865 (mpp) REVERT: K 306 MET cc_start: 0.8995 (mpp) cc_final: 0.8521 (mmm) REVERT: K 333 ASP cc_start: 0.7802 (p0) cc_final: 0.7451 (p0) REVERT: K 363 MET cc_start: 0.9179 (ptm) cc_final: 0.8725 (ppp) REVERT: K 485 LYS cc_start: 0.9226 (ttpt) cc_final: 0.8848 (ttpp) REVERT: K 607 GLN cc_start: 0.8577 (mt0) cc_final: 0.8303 (mt0) REVERT: L 180 MET cc_start: 0.8436 (mmm) cc_final: 0.8168 (mmm) REVERT: L 236 MET cc_start: 0.7181 (mmt) cc_final: 0.6534 (mmt) REVERT: L 284 MET cc_start: 0.8545 (mpp) cc_final: 0.8192 (mpp) REVERT: L 443 MET cc_start: 0.9136 (tpp) cc_final: 0.8279 (mmm) REVERT: L 607 GLN cc_start: 0.8459 (mt0) cc_final: 0.8156 (mt0) REVERT: L 609 PHE cc_start: 0.8749 (t80) cc_final: 0.8463 (t80) REVERT: L 642 PHE cc_start: 0.8904 (t80) cc_final: 0.8179 (t80) REVERT: M 180 MET cc_start: 0.8332 (mmm) cc_final: 0.8065 (mmm) REVERT: M 443 MET cc_start: 0.9072 (tpp) cc_final: 0.8741 (tpt) REVERT: M 485 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8583 (ttpt) REVERT: M 602 TYR cc_start: 0.8192 (t80) cc_final: 0.7944 (t80) REVERT: M 607 GLN cc_start: 0.8433 (mt0) cc_final: 0.8214 (mt0) REVERT: M 609 PHE cc_start: 0.8488 (t80) cc_final: 0.8188 (t80) REVERT: N 180 MET cc_start: 0.8446 (mmm) cc_final: 0.8144 (mmm) REVERT: N 284 MET cc_start: 0.8353 (mpp) cc_final: 0.7926 (mpp) REVERT: N 333 ASP cc_start: 0.7938 (p0) cc_final: 0.7697 (p0) REVERT: N 363 MET cc_start: 0.9165 (ptp) cc_final: 0.8951 (ptp) REVERT: N 607 GLN cc_start: 0.8558 (mt0) cc_final: 0.8025 (mt0) REVERT: O 180 MET cc_start: 0.8551 (mmm) cc_final: 0.8317 (mmm) REVERT: O 254 ASP cc_start: 0.8625 (m-30) cc_final: 0.8271 (t0) REVERT: O 284 MET cc_start: 0.8548 (mpp) cc_final: 0.8266 (mpp) REVERT: O 285 ILE cc_start: 0.8309 (mm) cc_final: 0.8039 (mm) REVERT: O 363 MET cc_start: 0.9267 (ptm) cc_final: 0.9032 (ppp) REVERT: O 443 MET cc_start: 0.8546 (tpp) cc_final: 0.8018 (tpt) REVERT: O 607 GLN cc_start: 0.8434 (mt0) cc_final: 0.7857 (mt0) REVERT: O 624 PRO cc_start: 0.8495 (Cg_endo) cc_final: 0.8233 (Cg_exo) outliers start: 19 outliers final: 0 residues processed: 1066 average time/residue: 0.4930 time to fit residues: 909.7672 Evaluate side-chains 676 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 676 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 2.9990 chunk 502 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 449 optimal weight: 4.9990 chunk 671 optimal weight: 0.8980 chunk 710 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 636 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 445 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 445 ASN D 445 ASN D 502 GLN E 241 ASN E 445 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 HIS F 640 GLN G 445 ASN ** H 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 445 ASN H 502 GLN H 640 GLN I 445 ASN ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 445 ASN J 502 GLN ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 ASN L 445 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 445 ASN ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 640 GLN N 211 ASN ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 ASN N 502 GLN O 340 GLN ** O 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 ASN ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.9501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 56790 Z= 0.470 Angle : 0.820 9.125 76755 Z= 0.439 Chirality : 0.052 0.185 9375 Planarity : 0.006 0.062 9975 Dihedral : 5.930 28.031 7800 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.94 % Favored : 96.05 % Rotamer: Outliers : 0.02 % Allowed : 5.98 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.09), residues: 7215 helix: 0.37 (0.11), residues: 2115 sheet: -0.35 (0.08), residues: 3180 loop : -0.57 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 419 HIS 0.004 0.001 HIS H 288 PHE 0.023 0.002 PHE C 450 TYR 0.021 0.003 TYR N 352 ARG 0.008 0.001 ARG M 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 708 time to evaluate : 4.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8240 (mmm) cc_final: 0.7991 (mmm) REVERT: A 242 ASN cc_start: 0.6691 (p0) cc_final: 0.6073 (p0) REVERT: A 284 MET cc_start: 0.8113 (mpp) cc_final: 0.7485 (mpp) REVERT: A 352 TYR cc_start: 0.8452 (m-10) cc_final: 0.8168 (m-10) REVERT: A 363 MET cc_start: 0.9289 (ptm) cc_final: 0.8299 (ppp) REVERT: A 443 MET cc_start: 0.9481 (tpp) cc_final: 0.8654 (tpp) REVERT: B 180 MET cc_start: 0.8538 (mmm) cc_final: 0.8203 (mmm) REVERT: B 284 MET cc_start: 0.7969 (mpp) cc_final: 0.7569 (mpp) REVERT: B 333 ASP cc_start: 0.8516 (p0) cc_final: 0.8242 (p0) REVERT: B 363 MET cc_start: 0.9102 (mtp) cc_final: 0.8673 (mmt) REVERT: B 443 MET cc_start: 0.9326 (tpp) cc_final: 0.8989 (mmm) REVERT: B 607 GLN cc_start: 0.8452 (mt0) cc_final: 0.7972 (mt0) REVERT: C 180 MET cc_start: 0.8042 (mmp) cc_final: 0.7759 (mmm) REVERT: C 284 MET cc_start: 0.7965 (mpp) cc_final: 0.7626 (mpp) REVERT: C 303 MET cc_start: 0.8304 (ttt) cc_final: 0.7975 (mtp) REVERT: C 306 MET cc_start: 0.9227 (mpp) cc_final: 0.8743 (mmp) REVERT: C 321 LEU cc_start: 0.9286 (tp) cc_final: 0.9015 (tp) REVERT: C 363 MET cc_start: 0.9288 (ptp) cc_final: 0.8869 (ptp) REVERT: C 607 GLN cc_start: 0.8379 (mt0) cc_final: 0.7841 (mt0) REVERT: D 180 MET cc_start: 0.8647 (mmm) cc_final: 0.8278 (mmm) REVERT: D 254 ASP cc_start: 0.8838 (m-30) cc_final: 0.8587 (t0) REVERT: D 284 MET cc_start: 0.8099 (mpp) cc_final: 0.7706 (mpp) REVERT: D 306 MET cc_start: 0.9267 (mpp) cc_final: 0.8707 (mmp) REVERT: D 352 TYR cc_start: 0.8241 (m-10) cc_final: 0.7968 (m-10) REVERT: D 363 MET cc_start: 0.9152 (mtp) cc_final: 0.8713 (mmm) REVERT: D 485 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8614 (ttmm) REVERT: D 501 GLU cc_start: 0.8669 (pm20) cc_final: 0.8429 (pm20) REVERT: D 503 GLU cc_start: 0.8162 (pp20) cc_final: 0.7755 (pp20) REVERT: D 535 LEU cc_start: 0.9464 (tp) cc_final: 0.9243 (tt) REVERT: D 639 ILE cc_start: 0.9006 (mm) cc_final: 0.8676 (tp) REVERT: E 180 MET cc_start: 0.8520 (mmm) cc_final: 0.8246 (mmm) REVERT: E 254 ASP cc_start: 0.8817 (m-30) cc_final: 0.8521 (t0) REVERT: E 284 MET cc_start: 0.8016 (mpp) cc_final: 0.7379 (mpp) REVERT: F 180 MET cc_start: 0.8481 (mmm) cc_final: 0.8232 (mmm) REVERT: F 254 ASP cc_start: 0.8772 (m-30) cc_final: 0.8558 (t0) REVERT: F 284 MET cc_start: 0.8029 (mpp) cc_final: 0.7577 (mpp) REVERT: F 303 MET cc_start: 0.8239 (ttt) cc_final: 0.7917 (mtm) REVERT: F 306 MET cc_start: 0.9275 (mpp) cc_final: 0.9069 (mtt) REVERT: F 352 TYR cc_start: 0.8545 (m-80) cc_final: 0.8128 (m-10) REVERT: F 363 MET cc_start: 0.9065 (mtm) cc_final: 0.8527 (mmm) REVERT: F 485 LYS cc_start: 0.8830 (ttmm) cc_final: 0.7881 (ttmm) REVERT: F 503 GLU cc_start: 0.8205 (pp20) cc_final: 0.7907 (pp20) REVERT: F 607 GLN cc_start: 0.8397 (mt0) cc_final: 0.7642 (mt0) REVERT: G 180 MET cc_start: 0.8396 (mmm) cc_final: 0.8084 (mmm) REVERT: G 284 MET cc_start: 0.7902 (mpp) cc_final: 0.7432 (mpp) REVERT: G 306 MET cc_start: 0.9234 (mpp) cc_final: 0.8895 (mtt) REVERT: G 352 TYR cc_start: 0.8686 (m-10) cc_final: 0.8421 (m-10) REVERT: G 363 MET cc_start: 0.9219 (ptp) cc_final: 0.8874 (ptp) REVERT: G 443 MET cc_start: 0.9324 (tpp) cc_final: 0.8918 (tpp) REVERT: H 180 MET cc_start: 0.8470 (mmm) cc_final: 0.8178 (mmm) REVERT: H 306 MET cc_start: 0.9272 (mpp) cc_final: 0.8726 (mmp) REVERT: H 503 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8116 (tm-30) REVERT: H 607 GLN cc_start: 0.8237 (mt0) cc_final: 0.7795 (mt0) REVERT: I 180 MET cc_start: 0.8426 (mmm) cc_final: 0.8210 (mmm) REVERT: I 284 MET cc_start: 0.8200 (mpp) cc_final: 0.7484 (mpp) REVERT: I 329 MET cc_start: 0.9016 (mtm) cc_final: 0.8461 (mtm) REVERT: I 363 MET cc_start: 0.9107 (mtm) cc_final: 0.8617 (mtm) REVERT: I 503 GLU cc_start: 0.8160 (pp20) cc_final: 0.7811 (pp20) REVERT: I 607 GLN cc_start: 0.8552 (mt0) cc_final: 0.8224 (mt0) REVERT: J 180 MET cc_start: 0.8665 (mmm) cc_final: 0.8308 (mmm) REVERT: J 284 MET cc_start: 0.7921 (mpp) cc_final: 0.7355 (mpp) REVERT: J 306 MET cc_start: 0.9245 (mpp) cc_final: 0.8853 (mmt) REVERT: J 363 MET cc_start: 0.9178 (ptm) cc_final: 0.8692 (ppp) REVERT: J 485 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8919 (ttmt) REVERT: J 607 GLN cc_start: 0.8668 (mt0) cc_final: 0.8279 (mm-40) REVERT: K 180 MET cc_start: 0.8302 (mmm) cc_final: 0.7968 (mmm) REVERT: K 284 MET cc_start: 0.8064 (mpp) cc_final: 0.7590 (mpp) REVERT: K 306 MET cc_start: 0.9341 (mpp) cc_final: 0.8727 (mmp) REVERT: K 329 MET cc_start: 0.8767 (mtp) cc_final: 0.8368 (tmm) REVERT: K 531 ASP cc_start: 0.8050 (p0) cc_final: 0.7802 (t70) REVERT: L 180 MET cc_start: 0.8511 (mmm) cc_final: 0.8266 (mmm) REVERT: L 284 MET cc_start: 0.8096 (mpp) cc_final: 0.7823 (mpp) REVERT: L 363 MET cc_start: 0.9067 (mtp) cc_final: 0.8758 (mmm) REVERT: L 443 MET cc_start: 0.9314 (tpp) cc_final: 0.9045 (tpt) REVERT: L 642 PHE cc_start: 0.9250 (t80) cc_final: 0.8913 (t80) REVERT: M 180 MET cc_start: 0.8479 (mmm) cc_final: 0.8240 (mmm) REVERT: M 306 MET cc_start: 0.9244 (mpp) cc_final: 0.8823 (mmp) REVERT: M 363 MET cc_start: 0.9195 (ptm) cc_final: 0.8818 (ppp) REVERT: M 485 LYS cc_start: 0.8935 (ttmt) cc_final: 0.7936 (ttpt) REVERT: M 501 GLU cc_start: 0.8582 (pm20) cc_final: 0.8265 (pm20) REVERT: M 607 GLN cc_start: 0.8518 (mt0) cc_final: 0.7921 (mt0) REVERT: N 180 MET cc_start: 0.8477 (mmm) cc_final: 0.8225 (mmm) REVERT: N 255 LEU cc_start: 0.9211 (tp) cc_final: 0.9008 (tp) REVERT: N 284 MET cc_start: 0.7780 (mpp) cc_final: 0.7248 (mpp) REVERT: N 296 LEU cc_start: 0.9395 (tp) cc_final: 0.8926 (pp) REVERT: N 303 MET cc_start: 0.8288 (ttt) cc_final: 0.8045 (ttt) REVERT: N 363 MET cc_start: 0.9269 (ptp) cc_final: 0.9041 (ptp) REVERT: N 535 LEU cc_start: 0.9462 (tp) cc_final: 0.9210 (tt) REVERT: N 607 GLN cc_start: 0.8194 (mt0) cc_final: 0.7455 (mt0) REVERT: O 284 MET cc_start: 0.7853 (mpp) cc_final: 0.7203 (mpp) REVERT: O 303 MET cc_start: 0.8009 (ttt) cc_final: 0.7590 (tmm) REVERT: O 306 MET cc_start: 0.9371 (mpp) cc_final: 0.9099 (mtt) REVERT: O 323 GLU cc_start: 0.8738 (pm20) cc_final: 0.8504 (pm20) REVERT: O 328 GLU cc_start: 0.8640 (tp30) cc_final: 0.8412 (tm-30) REVERT: O 329 MET cc_start: 0.8907 (mmm) cc_final: 0.8586 (mmt) REVERT: O 443 MET cc_start: 0.9285 (tpp) cc_final: 0.9017 (tpt) REVERT: O 609 PHE cc_start: 0.8971 (t80) cc_final: 0.8591 (t80) outliers start: 1 outliers final: 0 residues processed: 709 average time/residue: 0.4854 time to fit residues: 601.6115 Evaluate side-chains 544 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 528 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 606 optimal weight: 0.9980 chunk 491 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 362 optimal weight: 0.7980 chunk 637 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN D 242 ASN E 211 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN F 300 GLN ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN G 336 ASN H 361 ASN H 522 GLN ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 GLN L 502 GLN L 522 GLN ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 ASN N 300 GLN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 340 GLN ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.9847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56790 Z= 0.217 Angle : 0.656 8.977 76755 Z= 0.350 Chirality : 0.049 0.173 9375 Planarity : 0.004 0.047 9975 Dihedral : 5.270 24.691 7800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 7215 helix: 0.75 (0.11), residues: 2160 sheet: -0.12 (0.08), residues: 3120 loop : -0.51 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 419 HIS 0.002 0.000 HIS E 635 PHE 0.022 0.002 PHE C 609 TYR 0.025 0.002 TYR I 352 ARG 0.007 0.000 ARG J 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 723 time to evaluate : 5.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8238 (mmm) cc_final: 0.7963 (mmm) REVERT: A 284 MET cc_start: 0.7895 (mpp) cc_final: 0.7217 (mpp) REVERT: A 306 MET cc_start: 0.8886 (mtt) cc_final: 0.8557 (mmp) REVERT: A 443 MET cc_start: 0.9395 (tpp) cc_final: 0.9085 (mmm) REVERT: A 537 LEU cc_start: 0.9212 (mm) cc_final: 0.8957 (mm) REVERT: B 180 MET cc_start: 0.8567 (mmm) cc_final: 0.8212 (mmm) REVERT: B 284 MET cc_start: 0.7624 (mpp) cc_final: 0.7308 (mpp) REVERT: B 306 MET cc_start: 0.8935 (mtt) cc_final: 0.8654 (mmp) REVERT: B 363 MET cc_start: 0.9090 (mtp) cc_final: 0.8620 (mmm) REVERT: B 607 GLN cc_start: 0.8331 (mt0) cc_final: 0.8094 (mt0) REVERT: C 160 ASP cc_start: 0.3755 (t0) cc_final: 0.3060 (p0) REVERT: C 180 MET cc_start: 0.8068 (mmp) cc_final: 0.7729 (mmm) REVERT: C 185 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8533 (tm-30) REVERT: C 284 MET cc_start: 0.7871 (mpp) cc_final: 0.7510 (mpp) REVERT: C 301 ASP cc_start: 0.8498 (p0) cc_final: 0.8294 (p0) REVERT: C 306 MET cc_start: 0.9086 (mpp) cc_final: 0.8846 (mmp) REVERT: C 363 MET cc_start: 0.9255 (ptp) cc_final: 0.8936 (ptp) REVERT: D 180 MET cc_start: 0.8611 (mmm) cc_final: 0.8240 (mmm) REVERT: D 254 ASP cc_start: 0.8809 (m-30) cc_final: 0.8517 (t0) REVERT: D 284 MET cc_start: 0.7929 (mpp) cc_final: 0.7503 (mpp) REVERT: D 303 MET cc_start: 0.7825 (ttt) cc_final: 0.7405 (tmm) REVERT: D 306 MET cc_start: 0.8998 (mpp) cc_final: 0.8725 (mmp) REVERT: D 363 MET cc_start: 0.9032 (mtp) cc_final: 0.8788 (mtm) REVERT: D 639 ILE cc_start: 0.8959 (mm) cc_final: 0.8554 (tp) REVERT: E 180 MET cc_start: 0.8526 (mmm) cc_final: 0.8261 (mmm) REVERT: E 254 ASP cc_start: 0.8832 (m-30) cc_final: 0.8524 (t0) REVERT: E 284 MET cc_start: 0.7902 (mpp) cc_final: 0.7369 (mpp) REVERT: E 352 TYR cc_start: 0.7889 (m-10) cc_final: 0.7569 (m-10) REVERT: F 180 MET cc_start: 0.8438 (mmm) cc_final: 0.8166 (mmm) REVERT: F 185 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8085 (tm-30) REVERT: F 254 ASP cc_start: 0.8697 (m-30) cc_final: 0.8473 (t0) REVERT: F 284 MET cc_start: 0.7931 (mpp) cc_final: 0.7361 (mpp) REVERT: F 352 TYR cc_start: 0.8333 (m-80) cc_final: 0.8127 (m-10) REVERT: F 363 MET cc_start: 0.9082 (mtm) cc_final: 0.8449 (mmt) REVERT: F 537 LEU cc_start: 0.9096 (mm) cc_final: 0.8809 (mm) REVERT: G 180 MET cc_start: 0.8404 (mmm) cc_final: 0.8149 (mmm) REVERT: G 185 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8369 (tm-30) REVERT: G 284 MET cc_start: 0.7776 (mpp) cc_final: 0.7200 (mpp) REVERT: G 306 MET cc_start: 0.9031 (mpp) cc_final: 0.8786 (mmp) REVERT: G 363 MET cc_start: 0.9225 (ptp) cc_final: 0.8876 (ptp) REVERT: G 443 MET cc_start: 0.9246 (tpp) cc_final: 0.8811 (mmm) REVERT: H 180 MET cc_start: 0.8349 (mmm) cc_final: 0.8080 (mmm) REVERT: H 352 TYR cc_start: 0.7821 (m-10) cc_final: 0.7425 (m-10) REVERT: H 363 MET cc_start: 0.9113 (ptp) cc_final: 0.8869 (ptm) REVERT: H 503 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8131 (tm-30) REVERT: H 565 PHE cc_start: 0.9060 (m-80) cc_final: 0.8699 (m-80) REVERT: I 284 MET cc_start: 0.8018 (mpp) cc_final: 0.7468 (mpp) REVERT: I 306 MET cc_start: 0.8963 (mmp) cc_final: 0.8752 (mmp) REVERT: I 352 TYR cc_start: 0.7715 (m-10) cc_final: 0.7494 (m-10) REVERT: I 363 MET cc_start: 0.9045 (mtm) cc_final: 0.8621 (mtm) REVERT: I 485 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8558 (ttmt) REVERT: I 537 LEU cc_start: 0.9074 (mm) cc_final: 0.8852 (mm) REVERT: I 607 GLN cc_start: 0.8595 (mt0) cc_final: 0.8329 (mt0) REVERT: J 180 MET cc_start: 0.8690 (mmm) cc_final: 0.8355 (mmm) REVERT: J 284 MET cc_start: 0.7806 (mpp) cc_final: 0.7350 (mpp) REVERT: J 352 TYR cc_start: 0.7934 (m-10) cc_final: 0.7602 (m-10) REVERT: J 501 GLU cc_start: 0.8584 (pm20) cc_final: 0.8196 (pm20) REVERT: J 528 MET cc_start: 0.9365 (tpp) cc_final: 0.8757 (mmm) REVERT: J 607 GLN cc_start: 0.8597 (mt0) cc_final: 0.8065 (mt0) REVERT: K 180 MET cc_start: 0.8327 (mmm) cc_final: 0.7985 (mmm) REVERT: K 284 MET cc_start: 0.7930 (mpp) cc_final: 0.7441 (mpp) REVERT: K 306 MET cc_start: 0.9128 (mpp) cc_final: 0.8861 (mmp) REVERT: K 352 TYR cc_start: 0.7694 (m-10) cc_final: 0.7447 (m-10) REVERT: K 363 MET cc_start: 0.9085 (ptm) cc_final: 0.8591 (ppp) REVERT: K 531 ASP cc_start: 0.7888 (p0) cc_final: 0.7619 (t70) REVERT: K 607 GLN cc_start: 0.8492 (mt0) cc_final: 0.7980 (mt0) REVERT: L 180 MET cc_start: 0.8529 (mmm) cc_final: 0.8230 (mmm) REVERT: L 284 MET cc_start: 0.7890 (mpp) cc_final: 0.7447 (mpp) REVERT: L 363 MET cc_start: 0.9000 (mtp) cc_final: 0.8544 (mmm) REVERT: L 443 MET cc_start: 0.9210 (tpp) cc_final: 0.8916 (tpt) REVERT: L 485 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8239 (ttpp) REVERT: L 501 GLU cc_start: 0.8407 (pm20) cc_final: 0.7967 (pm20) REVERT: M 180 MET cc_start: 0.8507 (mmm) cc_final: 0.8244 (mmm) REVERT: M 211 ASN cc_start: 0.8285 (t0) cc_final: 0.8036 (t0) REVERT: M 284 MET cc_start: 0.8072 (mpp) cc_final: 0.7427 (mpp) REVERT: M 306 MET cc_start: 0.9131 (mpp) cc_final: 0.8909 (mmp) REVERT: M 363 MET cc_start: 0.9116 (ptm) cc_final: 0.8615 (ppp) REVERT: M 485 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8307 (ttmm) REVERT: N 180 MET cc_start: 0.8586 (mmm) cc_final: 0.8293 (mmm) REVERT: N 185 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8448 (tm-30) REVERT: N 284 MET cc_start: 0.7771 (mpp) cc_final: 0.7186 (mpp) REVERT: N 323 GLU cc_start: 0.8920 (pm20) cc_final: 0.8694 (pm20) REVERT: N 363 MET cc_start: 0.9127 (ptp) cc_final: 0.8847 (ptp) REVERT: N 485 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8558 (ttpp) REVERT: N 501 GLU cc_start: 0.8579 (pm20) cc_final: 0.8295 (pm20) REVERT: N 537 LEU cc_start: 0.9119 (mm) cc_final: 0.8899 (mm) REVERT: O 180 MET cc_start: 0.8010 (mmp) cc_final: 0.7709 (mmm) REVERT: O 284 MET cc_start: 0.7855 (mpp) cc_final: 0.7164 (mpp) REVERT: O 323 GLU cc_start: 0.8719 (pm20) cc_final: 0.8346 (pm20) REVERT: O 352 TYR cc_start: 0.7316 (m-10) cc_final: 0.6975 (m-10) REVERT: O 443 MET cc_start: 0.9130 (tpp) cc_final: 0.8838 (tpt) REVERT: O 485 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8404 (ttpt) REVERT: O 528 MET cc_start: 0.9087 (mmm) cc_final: 0.8841 (mmm) outliers start: 4 outliers final: 3 residues processed: 726 average time/residue: 0.4965 time to fit residues: 627.7410 Evaluate side-chains 584 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 581 time to evaluate : 4.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 0.5980 chunk 639 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 417 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 711 optimal weight: 4.9990 chunk 590 optimal weight: 9.9990 chunk 329 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 373 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN G 211 ASN ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 GLN H 374 GLN H 635 HIS ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 635 HIS ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 ASN ** N 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 640 GLN ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 1.0402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 56790 Z= 0.316 Angle : 0.686 6.909 76755 Z= 0.368 Chirality : 0.049 0.165 9375 Planarity : 0.005 0.043 9975 Dihedral : 5.316 24.499 7800 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 7215 helix: 0.82 (0.11), residues: 2175 sheet: -0.16 (0.08), residues: 3330 loop : -0.55 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 341 HIS 0.003 0.001 HIS J 288 PHE 0.024 0.002 PHE C 609 TYR 0.024 0.002 TYR I 352 ARG 0.005 0.001 ARG J 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 640 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8265 (mmm) cc_final: 0.8017 (mmm) REVERT: A 284 MET cc_start: 0.7839 (mpp) cc_final: 0.7409 (mpp) REVERT: A 303 MET cc_start: 0.9014 (mmt) cc_final: 0.8738 (mmm) REVERT: A 363 MET cc_start: 0.9259 (ptm) cc_final: 0.8334 (ppp) REVERT: B 180 MET cc_start: 0.8590 (mmm) cc_final: 0.8216 (mmm) REVERT: B 185 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8459 (tm-30) REVERT: B 284 MET cc_start: 0.7671 (mpp) cc_final: 0.7319 (mpp) REVERT: B 363 MET cc_start: 0.9046 (mtp) cc_final: 0.8559 (mmm) REVERT: B 443 MET cc_start: 0.8806 (ttt) cc_final: 0.8395 (ttt) REVERT: B 573 GLU cc_start: 0.9336 (pp20) cc_final: 0.9038 (tm-30) REVERT: C 180 MET cc_start: 0.8146 (mmp) cc_final: 0.7757 (mmm) REVERT: C 185 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8635 (tm-30) REVERT: C 306 MET cc_start: 0.9138 (mpp) cc_final: 0.8914 (mmp) REVERT: C 363 MET cc_start: 0.9180 (ptp) cc_final: 0.8841 (ptp) REVERT: C 443 MET cc_start: 0.9320 (tpp) cc_final: 0.9087 (mmm) REVERT: C 607 GLN cc_start: 0.8585 (tt0) cc_final: 0.8211 (tm-30) REVERT: D 180 MET cc_start: 0.8633 (mmm) cc_final: 0.8342 (mmm) REVERT: D 284 MET cc_start: 0.7809 (mpp) cc_final: 0.7450 (mpp) REVERT: D 303 MET cc_start: 0.8133 (ttt) cc_final: 0.7863 (ttt) REVERT: D 306 MET cc_start: 0.9049 (mpp) cc_final: 0.8730 (mmp) REVERT: D 363 MET cc_start: 0.9140 (mtp) cc_final: 0.8875 (mmm) REVERT: E 180 MET cc_start: 0.8515 (mmm) cc_final: 0.8255 (mmm) REVERT: E 254 ASP cc_start: 0.8935 (m-30) cc_final: 0.8571 (t70) REVERT: E 284 MET cc_start: 0.7875 (mpp) cc_final: 0.7488 (mpp) REVERT: E 363 MET cc_start: 0.9285 (ptp) cc_final: 0.9080 (ptm) REVERT: F 180 MET cc_start: 0.8438 (mmm) cc_final: 0.8180 (mmm) REVERT: F 185 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8189 (tm-30) REVERT: F 284 MET cc_start: 0.7852 (mpp) cc_final: 0.7356 (mpp) REVERT: F 363 MET cc_start: 0.8940 (mtm) cc_final: 0.8465 (mmm) REVERT: G 180 MET cc_start: 0.8466 (mmm) cc_final: 0.8148 (mmm) REVERT: G 185 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8546 (tm-30) REVERT: G 284 MET cc_start: 0.7553 (mpp) cc_final: 0.7254 (mpp) REVERT: G 363 MET cc_start: 0.9222 (ptp) cc_final: 0.8837 (ptp) REVERT: G 443 MET cc_start: 0.9267 (tpp) cc_final: 0.9036 (tpp) REVERT: G 528 MET cc_start: 0.9168 (mmm) cc_final: 0.8835 (mmt) REVERT: G 607 GLN cc_start: 0.8678 (mt0) cc_final: 0.8406 (mt0) REVERT: H 180 MET cc_start: 0.8319 (mmm) cc_final: 0.8104 (mmm) REVERT: H 236 MET cc_start: 0.6530 (mmt) cc_final: 0.6312 (mmm) REVERT: H 352 TYR cc_start: 0.8064 (m-10) cc_final: 0.7764 (m-10) REVERT: H 503 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8176 (tm-30) REVERT: I 180 MET cc_start: 0.8160 (mmp) cc_final: 0.7830 (mmm) REVERT: I 284 MET cc_start: 0.7655 (mpp) cc_final: 0.7308 (mpp) REVERT: I 290 ASP cc_start: 0.8737 (m-30) cc_final: 0.8371 (t0) REVERT: I 303 MET cc_start: 0.8760 (mmm) cc_final: 0.8530 (mmm) REVERT: I 363 MET cc_start: 0.9038 (mtm) cc_final: 0.8612 (mtm) REVERT: I 443 MET cc_start: 0.9295 (tpp) cc_final: 0.8684 (tpp) REVERT: I 503 GLU cc_start: 0.7931 (pp20) cc_final: 0.7595 (pp20) REVERT: J 180 MET cc_start: 0.8505 (mmm) cc_final: 0.8167 (mmm) REVERT: J 284 MET cc_start: 0.7853 (mpp) cc_final: 0.7390 (mpp) REVERT: J 306 MET cc_start: 0.9042 (mmt) cc_final: 0.8649 (mmp) REVERT: J 363 MET cc_start: 0.9340 (ptm) cc_final: 0.8638 (ppp) REVERT: J 501 GLU cc_start: 0.8295 (pm20) cc_final: 0.8071 (pm20) REVERT: J 607 GLN cc_start: 0.8613 (mt0) cc_final: 0.8350 (mt0) REVERT: K 180 MET cc_start: 0.8309 (mmm) cc_final: 0.8038 (mmm) REVERT: K 284 MET cc_start: 0.7556 (mpp) cc_final: 0.7312 (mpp) REVERT: K 303 MET cc_start: 0.8188 (ttt) cc_final: 0.7975 (tmm) REVERT: K 306 MET cc_start: 0.9147 (mpp) cc_final: 0.8756 (mmp) REVERT: K 352 TYR cc_start: 0.7902 (m-10) cc_final: 0.7685 (m-10) REVERT: K 363 MET cc_start: 0.9064 (ptm) cc_final: 0.8862 (ppp) REVERT: K 528 MET cc_start: 0.9237 (tpp) cc_final: 0.8870 (mmm) REVERT: K 543 GLU cc_start: 0.8952 (mp0) cc_final: 0.8752 (mp0) REVERT: L 180 MET cc_start: 0.8458 (mmm) cc_final: 0.8191 (mmm) REVERT: L 185 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8509 (tm-30) REVERT: L 284 MET cc_start: 0.7936 (mpp) cc_final: 0.7397 (mpp) REVERT: L 363 MET cc_start: 0.9000 (mtp) cc_final: 0.8664 (mmm) REVERT: L 443 MET cc_start: 0.9131 (tpp) cc_final: 0.8706 (tpp) REVERT: M 180 MET cc_start: 0.8509 (mmm) cc_final: 0.8293 (mmm) REVERT: M 284 MET cc_start: 0.7953 (mpp) cc_final: 0.7498 (mpp) REVERT: M 306 MET cc_start: 0.9230 (mpp) cc_final: 0.8995 (mmp) REVERT: N 180 MET cc_start: 0.8373 (mmm) cc_final: 0.8118 (mmm) REVERT: N 185 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8568 (tm-30) REVERT: N 284 MET cc_start: 0.7856 (mpp) cc_final: 0.7331 (mpp) REVERT: N 306 MET cc_start: 0.9112 (mtt) cc_final: 0.8636 (mmp) REVERT: N 485 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8494 (ttmm) REVERT: N 607 GLN cc_start: 0.8657 (mt0) cc_final: 0.8455 (mt0) REVERT: O 180 MET cc_start: 0.7823 (mmp) cc_final: 0.7468 (mmm) REVERT: O 284 MET cc_start: 0.7697 (mpp) cc_final: 0.7319 (mpp) REVERT: O 306 MET cc_start: 0.9209 (mmt) cc_final: 0.8554 (mmp) REVERT: O 323 GLU cc_start: 0.8829 (pm20) cc_final: 0.8593 (pm20) REVERT: O 363 MET cc_start: 0.9236 (ptm) cc_final: 0.8891 (ppp) REVERT: O 443 MET cc_start: 0.9308 (tpp) cc_final: 0.9040 (tpt) REVERT: O 485 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8357 (ttpt) REVERT: O 535 LEU cc_start: 0.9522 (tp) cc_final: 0.9312 (tt) outliers start: 1 outliers final: 0 residues processed: 641 average time/residue: 0.4800 time to fit residues: 541.2689 Evaluate side-chains 512 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 405 optimal weight: 0.8980 chunk 519 optimal weight: 10.0000 chunk 402 optimal weight: 20.0000 chunk 598 optimal weight: 4.9990 chunk 397 optimal weight: 8.9990 chunk 708 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 635 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 635 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 GLN ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 635 HIS ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 1.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 56790 Z= 0.392 Angle : 0.737 10.827 76755 Z= 0.395 Chirality : 0.049 0.182 9375 Planarity : 0.005 0.043 9975 Dihedral : 5.587 26.010 7800 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.09), residues: 7215 helix: 0.65 (0.11), residues: 2205 sheet: -0.17 (0.08), residues: 3315 loop : -0.94 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 419 HIS 0.002 0.001 HIS M 288 PHE 0.021 0.002 PHE M 609 TYR 0.028 0.002 TYR F 352 ARG 0.009 0.001 ARG I 544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 593 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8315 (mmm) cc_final: 0.8052 (mmm) REVERT: A 284 MET cc_start: 0.7757 (mpp) cc_final: 0.7431 (mpp) REVERT: A 290 ASP cc_start: 0.8708 (m-30) cc_final: 0.8506 (t0) REVERT: A 303 MET cc_start: 0.9102 (mmt) cc_final: 0.8851 (mmm) REVERT: A 329 MET cc_start: 0.8932 (mmm) cc_final: 0.8452 (mmt) REVERT: A 363 MET cc_start: 0.9132 (ptm) cc_final: 0.8480 (ppp) REVERT: B 180 MET cc_start: 0.8681 (mmm) cc_final: 0.8371 (mmm) REVERT: B 363 MET cc_start: 0.9175 (mtp) cc_final: 0.8858 (mmm) REVERT: B 368 GLU cc_start: 0.8683 (mp0) cc_final: 0.8463 (mp0) REVERT: B 443 MET cc_start: 0.8930 (ttt) cc_final: 0.8562 (ttt) REVERT: B 573 GLU cc_start: 0.9384 (pp20) cc_final: 0.9004 (tm-30) REVERT: B 607 GLN cc_start: 0.8182 (mt0) cc_final: 0.7647 (mt0) REVERT: B 642 PHE cc_start: 0.9184 (t80) cc_final: 0.8808 (t80) REVERT: C 180 MET cc_start: 0.8318 (mmp) cc_final: 0.7931 (mmm) REVERT: C 290 ASP cc_start: 0.8772 (m-30) cc_final: 0.8369 (t0) REVERT: C 352 TYR cc_start: 0.7593 (m-10) cc_final: 0.7371 (m-10) REVERT: C 363 MET cc_start: 0.9279 (ptp) cc_final: 0.9004 (ptp) REVERT: D 180 MET cc_start: 0.8644 (mmm) cc_final: 0.8340 (mmm) REVERT: D 284 MET cc_start: 0.7516 (mpp) cc_final: 0.7278 (mpp) REVERT: D 303 MET cc_start: 0.8324 (ttt) cc_final: 0.8120 (ttt) REVERT: D 306 MET cc_start: 0.8989 (mpp) cc_final: 0.8635 (mmp) REVERT: D 607 GLN cc_start: 0.8697 (tt0) cc_final: 0.8349 (tm-30) REVERT: E 180 MET cc_start: 0.8547 (mmm) cc_final: 0.8328 (mmm) REVERT: E 254 ASP cc_start: 0.8902 (m-30) cc_final: 0.8642 (t0) REVERT: E 284 MET cc_start: 0.7747 (mpp) cc_final: 0.7290 (mpp) REVERT: E 290 ASP cc_start: 0.8770 (m-30) cc_final: 0.8391 (t0) REVERT: F 180 MET cc_start: 0.8489 (mmm) cc_final: 0.8265 (mmm) REVERT: F 255 LEU cc_start: 0.9191 (tp) cc_final: 0.8941 (tp) REVERT: F 284 MET cc_start: 0.7797 (mpp) cc_final: 0.7395 (mpp) REVERT: F 363 MET cc_start: 0.9024 (mtm) cc_final: 0.8488 (mmt) REVERT: F 528 MET cc_start: 0.9311 (mmm) cc_final: 0.9109 (mmm) REVERT: F 537 LEU cc_start: 0.9127 (mm) cc_final: 0.8926 (mm) REVERT: G 180 MET cc_start: 0.8451 (mmm) cc_final: 0.8111 (mmm) REVERT: G 185 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8624 (tm-30) REVERT: G 363 MET cc_start: 0.9242 (ptp) cc_final: 0.8894 (ptp) REVERT: G 441 THR cc_start: 0.9399 (m) cc_final: 0.9126 (p) REVERT: G 443 MET cc_start: 0.9295 (tpp) cc_final: 0.8977 (tpp) REVERT: G 642 PHE cc_start: 0.9108 (t80) cc_final: 0.8836 (t80) REVERT: H 180 MET cc_start: 0.8366 (mmm) cc_final: 0.8153 (mmm) REVERT: H 363 MET cc_start: 0.9295 (ptm) cc_final: 0.8529 (ppp) REVERT: H 443 MET cc_start: 0.9400 (tpp) cc_final: 0.9175 (tpp) REVERT: H 503 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8191 (tm-30) REVERT: I 180 MET cc_start: 0.7984 (mmp) cc_final: 0.7666 (mmm) REVERT: I 290 ASP cc_start: 0.8749 (m-30) cc_final: 0.8471 (t0) REVERT: I 363 MET cc_start: 0.9041 (mtm) cc_final: 0.8589 (mtm) REVERT: I 443 MET cc_start: 0.9336 (tpp) cc_final: 0.8724 (tpp) REVERT: I 642 PHE cc_start: 0.8951 (t80) cc_final: 0.8557 (t80) REVERT: J 180 MET cc_start: 0.8645 (mmm) cc_final: 0.8375 (mmm) REVERT: J 284 MET cc_start: 0.7821 (mpp) cc_final: 0.7430 (mpp) REVERT: J 290 ASP cc_start: 0.8814 (m-30) cc_final: 0.8449 (t0) REVERT: J 306 MET cc_start: 0.9003 (mmt) cc_final: 0.8599 (mmp) REVERT: J 363 MET cc_start: 0.9234 (ptm) cc_final: 0.8530 (ppp) REVERT: J 501 GLU cc_start: 0.8194 (pm20) cc_final: 0.7991 (pm20) REVERT: J 502 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8659 (tm-30) REVERT: J 607 GLN cc_start: 0.8623 (mt0) cc_final: 0.8349 (mt0) REVERT: K 180 MET cc_start: 0.8376 (mmm) cc_final: 0.8124 (mmm) REVERT: K 290 ASP cc_start: 0.8718 (m-30) cc_final: 0.8488 (t0) REVERT: K 352 TYR cc_start: 0.8131 (m-10) cc_final: 0.7923 (m-10) REVERT: K 543 GLU cc_start: 0.8936 (mp0) cc_final: 0.8730 (mp0) REVERT: K 642 PHE cc_start: 0.9013 (t80) cc_final: 0.8619 (t80) REVERT: L 180 MET cc_start: 0.8575 (mmm) cc_final: 0.8319 (mmm) REVERT: L 284 MET cc_start: 0.7855 (mpp) cc_final: 0.7303 (mpp) REVERT: L 329 MET cc_start: 0.8899 (mmm) cc_final: 0.8509 (mmm) REVERT: L 352 TYR cc_start: 0.7936 (m-10) cc_final: 0.7712 (m-10) REVERT: L 363 MET cc_start: 0.9118 (mtp) cc_final: 0.8811 (mmm) REVERT: M 180 MET cc_start: 0.8621 (mmm) cc_final: 0.8371 (mmm) REVERT: M 284 MET cc_start: 0.7771 (mpp) cc_final: 0.7406 (mpp) REVERT: M 329 MET cc_start: 0.8763 (mmm) cc_final: 0.8371 (mmm) REVERT: M 363 MET cc_start: 0.9169 (ptm) cc_final: 0.8920 (ppp) REVERT: N 180 MET cc_start: 0.8660 (mmm) cc_final: 0.8431 (mmm) REVERT: N 284 MET cc_start: 0.7689 (mpp) cc_final: 0.7420 (mpp) REVERT: N 303 MET cc_start: 0.8234 (ttt) cc_final: 0.7810 (ttt) REVERT: N 502 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8672 (tm-30) REVERT: O 180 MET cc_start: 0.7989 (mmp) cc_final: 0.7636 (mmm) REVERT: O 303 MET cc_start: 0.8336 (ttt) cc_final: 0.7956 (tmm) REVERT: O 306 MET cc_start: 0.9075 (mmt) cc_final: 0.8531 (mmp) REVERT: O 363 MET cc_start: 0.9172 (ptm) cc_final: 0.8675 (ppp) REVERT: O 443 MET cc_start: 0.9405 (tpp) cc_final: 0.9058 (tpt) REVERT: O 485 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8323 (ttpt) REVERT: O 501 GLU cc_start: 0.8409 (pm20) cc_final: 0.8172 (pm20) REVERT: O 535 LEU cc_start: 0.9551 (tp) cc_final: 0.9287 (tt) outliers start: 1 outliers final: 0 residues processed: 593 average time/residue: 0.4767 time to fit residues: 495.5422 Evaluate side-chains 458 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 423 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 450 optimal weight: 20.0000 chunk 482 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 556 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN E 312 GLN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 HIS ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 300 GLN ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 640 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 1.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 56790 Z= 0.204 Angle : 0.657 10.025 76755 Z= 0.347 Chirality : 0.048 0.178 9375 Planarity : 0.004 0.056 9975 Dihedral : 5.102 24.442 7800 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.05 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 7215 helix: 0.77 (0.11), residues: 2280 sheet: -0.14 (0.08), residues: 3330 loop : -0.83 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 419 HIS 0.002 0.000 HIS E 635 PHE 0.019 0.001 PHE J 642 TYR 0.023 0.002 TYR B 134 ARG 0.008 0.000 ARG M 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 638 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7647 (mpp) cc_final: 0.7430 (mpp) REVERT: A 303 MET cc_start: 0.9046 (mmt) cc_final: 0.8764 (mmm) REVERT: A 363 MET cc_start: 0.9117 (ptm) cc_final: 0.8451 (ppp) REVERT: A 444 ASP cc_start: 0.8706 (t0) cc_final: 0.8478 (t0) REVERT: B 180 MET cc_start: 0.8588 (mmm) cc_final: 0.8305 (mmm) REVERT: B 306 MET cc_start: 0.9148 (mtt) cc_final: 0.8677 (mmp) REVERT: B 363 MET cc_start: 0.9011 (mtp) cc_final: 0.8623 (mmm) REVERT: B 443 MET cc_start: 0.8853 (ttt) cc_final: 0.8451 (ttt) REVERT: B 573 GLU cc_start: 0.9347 (pp20) cc_final: 0.9054 (tm-30) REVERT: B 642 PHE cc_start: 0.9165 (t80) cc_final: 0.8763 (t80) REVERT: C 180 MET cc_start: 0.8326 (mmp) cc_final: 0.7962 (mmm) REVERT: C 185 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8718 (tm-30) REVERT: C 352 TYR cc_start: 0.7497 (m-10) cc_final: 0.7268 (m-10) REVERT: C 363 MET cc_start: 0.9166 (ptp) cc_final: 0.8933 (ptp) REVERT: C 444 ASP cc_start: 0.8785 (t0) cc_final: 0.8552 (t0) REVERT: C 573 GLU cc_start: 0.9157 (pp20) cc_final: 0.8840 (tm-30) REVERT: D 180 MET cc_start: 0.8601 (mmm) cc_final: 0.8311 (mmm) REVERT: D 303 MET cc_start: 0.8242 (ttt) cc_final: 0.8021 (mtm) REVERT: D 441 THR cc_start: 0.9382 (m) cc_final: 0.8959 (p) REVERT: D 607 GLN cc_start: 0.8445 (tt0) cc_final: 0.8038 (tm-30) REVERT: E 180 MET cc_start: 0.8563 (mmm) cc_final: 0.8358 (mmm) REVERT: E 236 MET cc_start: 0.6600 (mpp) cc_final: 0.5977 (mmm) REVERT: E 254 ASP cc_start: 0.8968 (m-30) cc_final: 0.8740 (t0) REVERT: E 284 MET cc_start: 0.7625 (mpp) cc_final: 0.7256 (mpp) REVERT: E 290 ASP cc_start: 0.8647 (m-30) cc_final: 0.8333 (t0) REVERT: E 443 MET cc_start: 0.8829 (tpt) cc_final: 0.8385 (tpt) REVERT: F 180 MET cc_start: 0.8574 (mmm) cc_final: 0.8373 (mmm) REVERT: F 242 ASN cc_start: 0.6592 (p0) cc_final: 0.6370 (p0) REVERT: F 284 MET cc_start: 0.7713 (mpp) cc_final: 0.7247 (mpp) REVERT: F 290 ASP cc_start: 0.8746 (m-30) cc_final: 0.8361 (t0) REVERT: F 329 MET cc_start: 0.8873 (mmm) cc_final: 0.8529 (mmm) REVERT: F 363 MET cc_start: 0.9061 (mtm) cc_final: 0.8520 (mmt) REVERT: F 443 MET cc_start: 0.8905 (tpt) cc_final: 0.8459 (tmm) REVERT: F 528 MET cc_start: 0.9281 (mmm) cc_final: 0.9081 (mmm) REVERT: G 180 MET cc_start: 0.8481 (mmm) cc_final: 0.8167 (mmm) REVERT: G 242 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6631 (p0) REVERT: G 306 MET cc_start: 0.8952 (mmp) cc_final: 0.8729 (mmp) REVERT: G 363 MET cc_start: 0.9201 (ptp) cc_final: 0.8887 (ptp) REVERT: G 443 MET cc_start: 0.9266 (tpp) cc_final: 0.8970 (tpp) REVERT: G 642 PHE cc_start: 0.9075 (t80) cc_final: 0.8769 (t80) REVERT: H 180 MET cc_start: 0.8379 (mmm) cc_final: 0.8178 (mmm) REVERT: H 363 MET cc_start: 0.9295 (ptm) cc_final: 0.8877 (ppp) REVERT: H 443 MET cc_start: 0.9423 (tpp) cc_final: 0.9148 (mmm) REVERT: H 503 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8136 (tm-30) REVERT: H 537 LEU cc_start: 0.8872 (mm) cc_final: 0.8666 (mm) REVERT: I 180 MET cc_start: 0.8071 (mmp) cc_final: 0.7752 (mmm) REVERT: I 290 ASP cc_start: 0.8714 (m-30) cc_final: 0.8393 (t0) REVERT: I 303 MET cc_start: 0.8857 (mmm) cc_final: 0.8576 (mmm) REVERT: I 363 MET cc_start: 0.9023 (mtm) cc_final: 0.8658 (mtm) REVERT: I 642 PHE cc_start: 0.8867 (t80) cc_final: 0.8534 (t80) REVERT: J 180 MET cc_start: 0.8726 (mmm) cc_final: 0.8420 (mmm) REVERT: J 284 MET cc_start: 0.7511 (mpp) cc_final: 0.7101 (mpp) REVERT: J 290 ASP cc_start: 0.8779 (m-30) cc_final: 0.8394 (t0) REVERT: J 303 MET cc_start: 0.9019 (mmt) cc_final: 0.8695 (mmt) REVERT: J 306 MET cc_start: 0.8974 (mmt) cc_final: 0.8525 (mmp) REVERT: J 363 MET cc_start: 0.9294 (ptm) cc_final: 0.8851 (ppp) REVERT: J 528 MET cc_start: 0.9182 (tpp) cc_final: 0.8660 (mmm) REVERT: J 607 GLN cc_start: 0.8607 (mt0) cc_final: 0.8354 (tt0) REVERT: K 290 ASP cc_start: 0.8715 (m-30) cc_final: 0.8376 (t0) REVERT: K 443 MET cc_start: 0.9113 (tpp) cc_final: 0.8882 (tpp) REVERT: K 543 GLU cc_start: 0.8952 (mp0) cc_final: 0.8702 (mp0) REVERT: K 642 PHE cc_start: 0.9013 (t80) cc_final: 0.8598 (t80) REVERT: L 180 MET cc_start: 0.8574 (mmm) cc_final: 0.8334 (mmm) REVERT: L 236 MET cc_start: 0.6579 (mpp) cc_final: 0.6168 (mmm) REVERT: L 303 MET cc_start: 0.8095 (tpt) cc_final: 0.7786 (tpt) REVERT: L 363 MET cc_start: 0.8950 (mtp) cc_final: 0.8540 (mmm) REVERT: M 242 ASN cc_start: 0.6729 (p0) cc_final: 0.6387 (p0) REVERT: M 284 MET cc_start: 0.7857 (mpp) cc_final: 0.7511 (mpp) REVERT: M 303 MET cc_start: 0.9035 (mmt) cc_final: 0.8517 (mmm) REVERT: M 485 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8030 (ttpp) REVERT: M 501 GLU cc_start: 0.8479 (pm20) cc_final: 0.8090 (pm20) REVERT: N 180 MET cc_start: 0.8725 (mmm) cc_final: 0.8519 (mmm) REVERT: N 290 ASP cc_start: 0.8531 (m-30) cc_final: 0.7962 (t0) REVERT: N 303 MET cc_start: 0.8183 (ttt) cc_final: 0.7473 (mtp) REVERT: O 180 MET cc_start: 0.8067 (mmp) cc_final: 0.7760 (mmm) REVERT: O 303 MET cc_start: 0.8377 (ttt) cc_final: 0.7975 (tmm) REVERT: O 306 MET cc_start: 0.9007 (mmt) cc_final: 0.8457 (mmp) REVERT: O 363 MET cc_start: 0.9168 (ptm) cc_final: 0.8779 (ppp) REVERT: O 443 MET cc_start: 0.9252 (tpp) cc_final: 0.8928 (tpt) REVERT: O 642 PHE cc_start: 0.9142 (t80) cc_final: 0.8815 (t80) outliers start: 3 outliers final: 0 residues processed: 638 average time/residue: 0.4829 time to fit residues: 539.3115 Evaluate side-chains 511 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 510 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 10.0000 chunk 678 optimal weight: 1.9990 chunk 619 optimal weight: 6.9990 chunk 660 optimal weight: 1.9990 chunk 397 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 518 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 596 optimal weight: 9.9990 chunk 624 optimal weight: 0.9980 chunk 657 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 GLN H 312 GLN ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 GLN ** N 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 1.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56790 Z= 0.285 Angle : 0.685 9.522 76755 Z= 0.364 Chirality : 0.048 0.173 9375 Planarity : 0.004 0.056 9975 Dihedral : 5.191 25.167 7800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 0.03 % Allowed : 0.77 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 7215 helix: 0.79 (0.11), residues: 2250 sheet: -0.00 (0.09), residues: 3135 loop : -1.22 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 419 HIS 0.003 0.001 HIS I 288 PHE 0.020 0.002 PHE M 609 TYR 0.023 0.002 TYR H 134 ARG 0.008 0.000 ARG O 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 562 time to evaluate : 5.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8147 (mmp) cc_final: 0.7746 (mmm) REVERT: A 303 MET cc_start: 0.9080 (mmt) cc_final: 0.8808 (mmm) REVERT: A 306 MET cc_start: 0.9050 (mmp) cc_final: 0.8845 (mmp) REVERT: A 363 MET cc_start: 0.9086 (ptm) cc_final: 0.8869 (ptm) REVERT: A 444 ASP cc_start: 0.8836 (t0) cc_final: 0.8612 (t0) REVERT: A 537 LEU cc_start: 0.9196 (mm) cc_final: 0.8990 (mm) REVERT: B 180 MET cc_start: 0.8631 (mmm) cc_final: 0.8377 (mmm) REVERT: B 236 MET cc_start: 0.5643 (mpp) cc_final: 0.5035 (mmm) REVERT: B 303 MET cc_start: 0.9074 (mmt) cc_final: 0.8748 (mmm) REVERT: B 306 MET cc_start: 0.9121 (mtt) cc_final: 0.8640 (mmp) REVERT: B 352 TYR cc_start: 0.7529 (m-10) cc_final: 0.7280 (m-10) REVERT: B 363 MET cc_start: 0.9018 (mtp) cc_final: 0.8702 (mmm) REVERT: B 368 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8758 (tm-30) REVERT: B 573 GLU cc_start: 0.9393 (pp20) cc_final: 0.9030 (tm-30) REVERT: B 642 PHE cc_start: 0.9167 (t80) cc_final: 0.8950 (t80) REVERT: C 180 MET cc_start: 0.8365 (mmp) cc_final: 0.7966 (mmm) REVERT: C 185 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8747 (tm-30) REVERT: C 352 TYR cc_start: 0.7591 (m-10) cc_final: 0.7292 (m-10) REVERT: C 363 MET cc_start: 0.9171 (ptp) cc_final: 0.8907 (ptp) REVERT: D 180 MET cc_start: 0.8667 (mmm) cc_final: 0.8402 (mmm) REVERT: D 607 GLN cc_start: 0.8548 (tt0) cc_final: 0.8090 (tm-30) REVERT: E 254 ASP cc_start: 0.9032 (m-30) cc_final: 0.8779 (t0) REVERT: E 284 MET cc_start: 0.7698 (mpp) cc_final: 0.7312 (mpp) REVERT: E 290 ASP cc_start: 0.8737 (m-30) cc_final: 0.8311 (t0) REVERT: E 352 TYR cc_start: 0.7821 (m-10) cc_final: 0.7531 (m-10) REVERT: E 443 MET cc_start: 0.8830 (tpt) cc_final: 0.8474 (tpp) REVERT: F 255 LEU cc_start: 0.9360 (tp) cc_final: 0.9141 (tp) REVERT: F 284 MET cc_start: 0.7715 (mpp) cc_final: 0.7362 (mpp) REVERT: F 290 ASP cc_start: 0.8735 (m-30) cc_final: 0.8492 (t0) REVERT: F 303 MET cc_start: 0.9105 (mmt) cc_final: 0.8784 (mmm) REVERT: F 363 MET cc_start: 0.9081 (mtm) cc_final: 0.8556 (mmt) REVERT: F 443 MET cc_start: 0.8970 (tpt) cc_final: 0.8431 (tmm) REVERT: G 180 MET cc_start: 0.8497 (mmm) cc_final: 0.8226 (mmm) REVERT: G 290 ASP cc_start: 0.8893 (m-30) cc_final: 0.8057 (t0) REVERT: G 303 MET cc_start: 0.8750 (mmm) cc_final: 0.8543 (mmm) REVERT: G 352 TYR cc_start: 0.7776 (m-10) cc_final: 0.7576 (m-10) REVERT: G 363 MET cc_start: 0.9217 (ptp) cc_final: 0.8871 (ptp) REVERT: G 441 THR cc_start: 0.9339 (m) cc_final: 0.9048 (p) REVERT: G 642 PHE cc_start: 0.9079 (t80) cc_final: 0.8714 (t80) REVERT: H 180 MET cc_start: 0.8431 (mmm) cc_final: 0.8185 (mmm) REVERT: H 303 MET cc_start: 0.8912 (mmm) cc_final: 0.8668 (mmm) REVERT: H 363 MET cc_start: 0.9207 (ptm) cc_final: 0.8993 (ppp) REVERT: H 503 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8173 (tm-30) REVERT: I 180 MET cc_start: 0.7960 (mmp) cc_final: 0.7600 (mmm) REVERT: I 290 ASP cc_start: 0.8784 (m-30) cc_final: 0.8468 (t0) REVERT: I 352 TYR cc_start: 0.7684 (m-10) cc_final: 0.7408 (m-10) REVERT: I 363 MET cc_start: 0.8994 (mtm) cc_final: 0.8671 (mtm) REVERT: I 642 PHE cc_start: 0.8837 (t80) cc_final: 0.8505 (t80) REVERT: J 180 MET cc_start: 0.8791 (mmm) cc_final: 0.8586 (mmm) REVERT: J 284 MET cc_start: 0.7378 (mpp) cc_final: 0.7035 (mpp) REVERT: J 290 ASP cc_start: 0.8807 (m-30) cc_final: 0.8512 (t0) REVERT: J 303 MET cc_start: 0.9080 (mmt) cc_final: 0.8823 (mmt) REVERT: J 306 MET cc_start: 0.8993 (mmt) cc_final: 0.8538 (mmp) REVERT: J 352 TYR cc_start: 0.7699 (m-10) cc_final: 0.7390 (m-10) REVERT: J 363 MET cc_start: 0.9188 (ptm) cc_final: 0.8926 (ppp) REVERT: J 528 MET cc_start: 0.9200 (tpp) cc_final: 0.8745 (mmm) REVERT: K 180 MET cc_start: 0.8301 (mmp) cc_final: 0.8003 (mmm) REVERT: K 290 ASP cc_start: 0.8735 (m-30) cc_final: 0.8308 (t0) REVERT: K 303 MET cc_start: 0.7827 (ttt) cc_final: 0.7568 (tmm) REVERT: K 363 MET cc_start: 0.9125 (ptm) cc_final: 0.8567 (ppp) REVERT: K 543 GLU cc_start: 0.8894 (mp0) cc_final: 0.8664 (mp0) REVERT: K 607 GLN cc_start: 0.8681 (tt0) cc_final: 0.8265 (tm-30) REVERT: K 642 PHE cc_start: 0.9014 (t80) cc_final: 0.8564 (t80) REVERT: L 180 MET cc_start: 0.8639 (mmm) cc_final: 0.8351 (mmm) REVERT: L 236 MET cc_start: 0.6519 (mpp) cc_final: 0.6180 (mmm) REVERT: L 303 MET cc_start: 0.8340 (tpt) cc_final: 0.8031 (tpt) REVERT: L 306 MET cc_start: 0.8971 (mmp) cc_final: 0.8769 (mmp) REVERT: L 363 MET cc_start: 0.9065 (mtp) cc_final: 0.8772 (mmm) REVERT: L 443 MET cc_start: 0.9061 (tpp) cc_final: 0.8477 (tpp) REVERT: M 180 MET cc_start: 0.8350 (mmp) cc_final: 0.8073 (mmm) REVERT: M 284 MET cc_start: 0.7575 (mpp) cc_final: 0.7275 (mpp) REVERT: M 303 MET cc_start: 0.9035 (mmt) cc_final: 0.8501 (mmm) REVERT: M 363 MET cc_start: 0.8722 (ppp) cc_final: 0.8347 (ppp) REVERT: N 180 MET cc_start: 0.8704 (mmm) cc_final: 0.8432 (mmm) REVERT: N 290 ASP cc_start: 0.8624 (m-30) cc_final: 0.8086 (t0) REVERT: N 303 MET cc_start: 0.8238 (ttt) cc_final: 0.7547 (mtp) REVERT: N 363 MET cc_start: 0.9195 (ptp) cc_final: 0.8982 (ptp) REVERT: O 180 MET cc_start: 0.8103 (mmp) cc_final: 0.7790 (mmm) REVERT: O 303 MET cc_start: 0.8522 (ttt) cc_final: 0.8009 (tmm) REVERT: O 306 MET cc_start: 0.9009 (mmt) cc_final: 0.8485 (mmp) REVERT: O 352 TYR cc_start: 0.7102 (m-10) cc_final: 0.6554 (m-10) REVERT: O 363 MET cc_start: 0.9129 (ptm) cc_final: 0.8696 (ppp) REVERT: O 642 PHE cc_start: 0.9167 (t80) cc_final: 0.8787 (t80) outliers start: 2 outliers final: 0 residues processed: 562 average time/residue: 0.4862 time to fit residues: 482.6063 Evaluate side-chains 457 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 1.9990 chunk 698 optimal weight: 0.2980 chunk 426 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 485 optimal weight: 4.9990 chunk 732 optimal weight: 0.0370 chunk 673 optimal weight: 0.9980 chunk 583 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 chunk 357 optimal weight: 4.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS E 242 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 GLN ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 1.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 56790 Z= 0.214 Angle : 0.659 9.989 76755 Z= 0.348 Chirality : 0.048 0.172 9375 Planarity : 0.004 0.049 9975 Dihedral : 5.007 24.459 7800 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.05 % Allowed : 0.16 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 7215 helix: 0.81 (0.11), residues: 2265 sheet: 0.00 (0.09), residues: 3165 loop : -1.07 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 419 HIS 0.002 0.000 HIS M 288 PHE 0.021 0.001 PHE M 609 TYR 0.018 0.001 TYR I 352 ARG 0.006 0.000 ARG J 604 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14430 Ramachandran restraints generated. 7215 Oldfield, 0 Emsley, 7215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 588 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8200 (mmp) cc_final: 0.7797 (mmm) REVERT: A 303 MET cc_start: 0.9076 (mmt) cc_final: 0.8796 (mmm) REVERT: A 363 MET cc_start: 0.9072 (ptm) cc_final: 0.8787 (ppp) REVERT: A 444 ASP cc_start: 0.8612 (t0) cc_final: 0.8325 (t0) REVERT: B 180 MET cc_start: 0.8624 (mmm) cc_final: 0.8343 (mmm) REVERT: B 236 MET cc_start: 0.5715 (mpp) cc_final: 0.5076 (mmm) REVERT: B 306 MET cc_start: 0.9051 (mtt) cc_final: 0.8749 (mmp) REVERT: B 363 MET cc_start: 0.8965 (mtp) cc_final: 0.8512 (mmm) REVERT: B 368 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8728 (tm-30) REVERT: B 444 ASP cc_start: 0.8995 (t0) cc_final: 0.8723 (t0) REVERT: B 642 PHE cc_start: 0.9169 (t80) cc_final: 0.8958 (t80) REVERT: C 180 MET cc_start: 0.8386 (mmp) cc_final: 0.8135 (mmm) REVERT: C 236 MET cc_start: 0.6412 (mpp) cc_final: 0.6159 (mmp) REVERT: C 323 GLU cc_start: 0.8757 (pm20) cc_final: 0.8551 (pm20) REVERT: C 444 ASP cc_start: 0.8713 (t0) cc_final: 0.8504 (t0) REVERT: C 573 GLU cc_start: 0.9161 (pp20) cc_final: 0.8862 (tm-30) REVERT: D 441 THR cc_start: 0.9401 (m) cc_final: 0.8929 (p) REVERT: D 607 GLN cc_start: 0.8524 (tt0) cc_final: 0.8037 (tm-30) REVERT: E 236 MET cc_start: 0.6451 (mpp) cc_final: 0.5937 (mmm) REVERT: E 254 ASP cc_start: 0.9006 (m-30) cc_final: 0.8740 (t0) REVERT: E 290 ASP cc_start: 0.8660 (m-30) cc_final: 0.8334 (t0) REVERT: E 443 MET cc_start: 0.8759 (tpt) cc_final: 0.8370 (tpp) REVERT: E 537 LEU cc_start: 0.9103 (mm) cc_final: 0.8879 (mm) REVERT: E 646 MET cc_start: 0.7146 (tpp) cc_final: 0.6409 (mmm) REVERT: F 180 MET cc_start: 0.8304 (mmp) cc_final: 0.8000 (mmm) REVERT: F 284 MET cc_start: 0.7659 (mpp) cc_final: 0.7332 (mpp) REVERT: F 290 ASP cc_start: 0.8684 (m-30) cc_final: 0.8410 (t0) REVERT: F 303 MET cc_start: 0.9029 (mmt) cc_final: 0.8716 (mmm) REVERT: F 363 MET cc_start: 0.9103 (mtm) cc_final: 0.8596 (mmm) REVERT: F 397 TYR cc_start: 0.8406 (m-80) cc_final: 0.8132 (m-80) REVERT: F 443 MET cc_start: 0.8826 (tpt) cc_final: 0.8340 (tmm) REVERT: F 528 MET cc_start: 0.9245 (mmm) cc_final: 0.8973 (mmm) REVERT: F 642 PHE cc_start: 0.8924 (t80) cc_final: 0.8634 (t80) REVERT: G 180 MET cc_start: 0.8608 (mmm) cc_final: 0.8392 (mmm) REVERT: G 236 MET cc_start: 0.5911 (mpp) cc_final: 0.4481 (mmm) REVERT: G 290 ASP cc_start: 0.8797 (m-30) cc_final: 0.7952 (t0) REVERT: G 303 MET cc_start: 0.8756 (mmm) cc_final: 0.8536 (mmm) REVERT: G 363 MET cc_start: 0.9155 (ptp) cc_final: 0.8854 (ptp) REVERT: G 441 THR cc_start: 0.9318 (m) cc_final: 0.9087 (p) REVERT: G 642 PHE cc_start: 0.9054 (t80) cc_final: 0.8669 (t80) REVERT: H 303 MET cc_start: 0.8869 (mmm) cc_final: 0.8606 (mmm) REVERT: H 363 MET cc_start: 0.9162 (ptm) cc_final: 0.8944 (ppp) REVERT: H 503 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8153 (tm-30) REVERT: H 528 MET cc_start: 0.9304 (tpp) cc_final: 0.8871 (mmm) REVERT: I 180 MET cc_start: 0.8108 (mmp) cc_final: 0.7766 (mmm) REVERT: I 236 MET cc_start: 0.5809 (mpp) cc_final: 0.5338 (mmp) REVERT: I 290 ASP cc_start: 0.8736 (m-30) cc_final: 0.8413 (t0) REVERT: I 303 MET cc_start: 0.8908 (mmm) cc_final: 0.8686 (mmm) REVERT: I 352 TYR cc_start: 0.7505 (m-10) cc_final: 0.7261 (m-10) REVERT: I 363 MET cc_start: 0.9008 (mtm) cc_final: 0.8672 (mtm) REVERT: I 443 MET cc_start: 0.9118 (tpt) cc_final: 0.8652 (tpt) REVERT: I 455 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7314 (mm-30) REVERT: I 503 GLU cc_start: 0.7576 (pp20) cc_final: 0.7113 (pp20) REVERT: I 642 PHE cc_start: 0.8823 (t80) cc_final: 0.8470 (t80) REVERT: J 180 MET cc_start: 0.8771 (mmm) cc_final: 0.8546 (mmm) REVERT: J 284 MET cc_start: 0.7455 (mpp) cc_final: 0.7125 (mpp) REVERT: J 303 MET cc_start: 0.9070 (mmt) cc_final: 0.8803 (mmt) REVERT: J 306 MET cc_start: 0.8983 (mmt) cc_final: 0.8539 (mmp) REVERT: J 352 TYR cc_start: 0.7593 (m-10) cc_final: 0.7296 (m-10) REVERT: J 363 MET cc_start: 0.9151 (ptm) cc_final: 0.8893 (ppp) REVERT: J 528 MET cc_start: 0.9264 (tpp) cc_final: 0.8787 (mmm) REVERT: J 535 LEU cc_start: 0.9290 (tt) cc_final: 0.9064 (tt) REVERT: J 607 GLN cc_start: 0.8645 (tt0) cc_final: 0.8259 (tm-30) REVERT: K 180 MET cc_start: 0.8258 (mmp) cc_final: 0.7986 (mmm) REVERT: K 236 MET cc_start: 0.5410 (mpp) cc_final: 0.4812 (mmm) REVERT: K 303 MET cc_start: 0.7765 (ttt) cc_final: 0.7485 (tmm) REVERT: K 363 MET cc_start: 0.9034 (ptm) cc_final: 0.8775 (ppp) REVERT: K 443 MET cc_start: 0.9251 (tpp) cc_final: 0.9025 (tpp) REVERT: K 543 GLU cc_start: 0.8945 (mp0) cc_final: 0.8697 (mp0) REVERT: K 607 GLN cc_start: 0.8748 (tt0) cc_final: 0.8327 (tm-30) REVERT: K 642 PHE cc_start: 0.8970 (t80) cc_final: 0.8750 (t80) REVERT: L 180 MET cc_start: 0.8635 (mmm) cc_final: 0.8339 (mmm) REVERT: L 236 MET cc_start: 0.6570 (mpp) cc_final: 0.6241 (mmm) REVERT: L 303 MET cc_start: 0.8128 (tpt) cc_final: 0.7835 (tpt) REVERT: L 306 MET cc_start: 0.8967 (mmp) cc_final: 0.8760 (mmp) REVERT: L 363 MET cc_start: 0.9040 (mtp) cc_final: 0.8749 (mmm) REVERT: L 537 LEU cc_start: 0.9079 (mm) cc_final: 0.8869 (mm) REVERT: M 284 MET cc_start: 0.7460 (mpp) cc_final: 0.7174 (mpp) REVERT: M 290 ASP cc_start: 0.8734 (m-30) cc_final: 0.8311 (t0) REVERT: M 303 MET cc_start: 0.8975 (mmt) cc_final: 0.8429 (mmm) REVERT: M 363 MET cc_start: 0.8608 (ppp) cc_final: 0.8164 (ppp) REVERT: M 455 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7106 (mm-30) REVERT: M 501 GLU cc_start: 0.8328 (pp20) cc_final: 0.8116 (pm20) REVERT: N 180 MET cc_start: 0.8723 (mmm) cc_final: 0.8482 (mmm) REVERT: N 236 MET cc_start: 0.6184 (mpp) cc_final: 0.5362 (mmm) REVERT: N 303 MET cc_start: 0.8210 (ttt) cc_final: 0.7722 (mtm) REVERT: N 352 TYR cc_start: 0.7211 (m-10) cc_final: 0.7009 (m-10) REVERT: O 180 MET cc_start: 0.8146 (mmp) cc_final: 0.7830 (mmm) REVERT: O 306 MET cc_start: 0.8989 (mmt) cc_final: 0.8425 (mmp) REVERT: O 329 MET cc_start: 0.8575 (mmm) cc_final: 0.8294 (mmt) REVERT: O 352 TYR cc_start: 0.7156 (m-10) cc_final: 0.6730 (m-10) REVERT: O 642 PHE cc_start: 0.9136 (t80) cc_final: 0.8744 (t80) outliers start: 3 outliers final: 0 residues processed: 588 average time/residue: 0.4768 time to fit residues: 494.4215 Evaluate side-chains 485 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 0.9990 chunk 621 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 537 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 584 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 599 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN ** G 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 GLN ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068207 restraints weight = 191278.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069611 restraints weight = 120325.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.070544 restraints weight = 87417.280| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 1.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 56790 Z= 0.234 Angle : 0.664 12.882 76755 Z= 0.350 Chirality : 0.048 0.180 9375 Planarity : 0.004 0.050 9975 Dihedral : 4.997 24.054 7800 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 7215 helix: 0.73 (0.11), residues: 2295 sheet: -0.09 (0.09), residues: 3255 loop : -0.83 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 419 HIS 0.002 0.000 HIS E 635 PHE 0.020 0.001 PHE M 609 TYR 0.018 0.001 TYR I 352 ARG 0.006 0.000 ARG N 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11731.57 seconds wall clock time: 207 minutes 22.09 seconds (12442.09 seconds total)