Starting phenix.real_space_refine on Mon Mar 11 04:46:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5x_17456/03_2024/8p5x_17456_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5x_17456/03_2024/8p5x_17456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5x_17456/03_2024/8p5x_17456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5x_17456/03_2024/8p5x_17456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5x_17456/03_2024/8p5x_17456_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5x_17456/03_2024/8p5x_17456_updated.pdb" } resolution = 2.29 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= 0.020 sd= 1.252 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 222 5.16 5 C 34828 2.51 5 N 9755 2.21 5 O 10523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "A GLU 1220": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B GLU 929": "OE1" <-> "OE2" Residue "B GLU 1147": "OE1" <-> "OE2" Residue "B GLU 1156": "OE1" <-> "OE2" Residue "B GLU 1157": "OE1" <-> "OE2" Residue "B GLU 1164": "OE1" <-> "OE2" Residue "B GLU 1217": "OE1" <-> "OE2" Residue "B GLU 1220": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 656": "OE1" <-> "OE2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C GLU 923": "OE1" <-> "OE2" Residue "C GLU 929": "OE1" <-> "OE2" Residue "C GLU 1147": "OE1" <-> "OE2" Residue "C GLU 1156": "OE1" <-> "OE2" Residue "C GLU 1157": "OE1" <-> "OE2" Residue "C GLU 1164": "OE1" <-> "OE2" Residue "C GLU 1217": "OE1" <-> "OE2" Residue "C GLU 1220": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 656": "OE1" <-> "OE2" Residue "D ARG 767": "NH1" <-> "NH2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D GLU 923": "OE1" <-> "OE2" Residue "D GLU 929": "OE1" <-> "OE2" Residue "D GLU 1147": "OE1" <-> "OE2" Residue "D GLU 1156": "OE1" <-> "OE2" Residue "D GLU 1157": "OE1" <-> "OE2" Residue "D GLU 1164": "OE1" <-> "OE2" Residue "D GLU 1217": "OE1" <-> "OE2" Residue "D GLU 1220": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E ARG 317": "NH1" <-> "NH2" Residue "E GLU 432": "OE1" <-> "OE2" Residue "E GLU 587": "OE1" <-> "OE2" Residue "E PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 656": "OE1" <-> "OE2" Residue "E ARG 767": "NH1" <-> "NH2" Residue "E GLU 842": "OE1" <-> "OE2" Residue "E GLU 873": "OE1" <-> "OE2" Residue "E GLU 923": "OE1" <-> "OE2" Residue "E GLU 929": "OE1" <-> "OE2" Residue "E GLU 1147": "OE1" <-> "OE2" Residue "E GLU 1156": "OE1" <-> "OE2" Residue "E GLU 1157": "OE1" <-> "OE2" Residue "E GLU 1164": "OE1" <-> "OE2" Residue "E GLU 1217": "OE1" <-> "OE2" Residue "E GLU 1220": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F ARG 317": "NH1" <-> "NH2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 656": "OE1" <-> "OE2" Residue "F ARG 767": "NH1" <-> "NH2" Residue "F GLU 842": "OE1" <-> "OE2" Residue "F GLU 873": "OE1" <-> "OE2" Residue "F GLU 923": "OE1" <-> "OE2" Residue "F GLU 929": "OE1" <-> "OE2" Residue "F GLU 1147": "OE1" <-> "OE2" Residue "F GLU 1156": "OE1" <-> "OE2" Residue "F GLU 1157": "OE1" <-> "OE2" Residue "F GLU 1164": "OE1" <-> "OE2" Residue "F GLU 1217": "OE1" <-> "OE2" Residue "F GLU 1220": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55346 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 8400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8400 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 8404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8404 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "H" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "I" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "J" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.82, per 1000 atoms: 0.39 Number of scatterers: 55346 At special positions: 0 Unit cell: (227.9, 227.04, 171.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 222 16.00 P 12 15.00 Mg 6 11.99 O 10523 8.00 N 9755 7.00 C 34828 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: 14.40 Conformation dependent library (CDL) restraints added in 7.5 seconds 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 300 helices and 48 sheets defined 39.7% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.65 Creating SS restraints... Processing helix chain 'A' and resid 110 through 123 removed outlier: 3.977A pdb=" N LEU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.614A pdb=" N ARG A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.514A pdb=" N ILE A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 321 through 336 removed outlier: 3.825A pdb=" N THR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 368 through 386 removed outlier: 6.843A pdb=" N HIS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 409 through 412 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.646A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 516 through 532 Proline residue: A 520 - end of helix removed outlier: 3.795A pdb=" N ASP A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 525 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 526 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 558 through 561 No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.132A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 714 through 731 removed outlier: 3.513A pdb=" N ARG A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 760 through 764 Processing helix chain 'A' and resid 770 through 778 Processing helix chain 'A' and resid 786 through 803 removed outlier: 3.566A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.564A pdb=" N ALA A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 removed outlier: 4.223A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 950 through 962 removed outlier: 3.509A pdb=" N GLU A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 removed outlier: 4.267A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 982 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 983 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 986 " --> pdb=" O THR A 983 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 987 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 1022 through 1028 removed outlier: 3.677A pdb=" N LEU A1028 " --> pdb=" O ARG A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1079 through 1082 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1112 through 1124 removed outlier: 3.643A pdb=" N ALA A1118 " --> pdb=" O TYR A1115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A1124 " --> pdb=" O LYS A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1150 Processing helix chain 'A' and resid 1171 through 1181 removed outlier: 3.728A pdb=" N GLU A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Proline residue: A1179 - end of helix Processing helix chain 'A' and resid 1204 through 1219 Processing helix chain 'B' and resid 110 through 123 removed outlier: 3.978A pdb=" N LEU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.616A pdb=" N ARG B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.514A pdb=" N ILE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.825A pdb=" N THR B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 368 through 386 removed outlier: 6.842A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 409 through 412 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.646A pdb=" N LEU B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 503 Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 516 through 532 Proline residue: B 520 - end of helix removed outlier: 3.793A pdb=" N ASP B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 525 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 526 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 558 through 561 No H-bonds generated for 'chain 'B' and resid 558 through 561' Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 653 through 660 removed outlier: 4.134A pdb=" N LEU B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 714 through 731 removed outlier: 3.513A pdb=" N ARG B 729 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 760 through 764 Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 786 through 803 removed outlier: 3.567A pdb=" N ALA B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS B 797 " --> pdb=" O VAL B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 847 removed outlier: 3.566A pdb=" N ALA B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 removed outlier: 4.226A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 926 through 933 Processing helix chain 'B' and resid 950 through 962 removed outlier: 3.509A pdb=" N GLU B 956 " --> pdb=" O GLY B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 987 removed outlier: 4.268A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 982 " --> pdb=" O ASN B 979 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR B 983 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 986 " --> pdb=" O THR B 983 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 987 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 996 Processing helix chain 'B' and resid 1022 through 1028 removed outlier: 3.677A pdb=" N LEU B1028 " --> pdb=" O ARG B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1079 through 1082 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1112 through 1124 removed outlier: 3.642A pdb=" N ALA B1118 " --> pdb=" O TYR B1115 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP B1124 " --> pdb=" O LYS B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1150 Processing helix chain 'B' and resid 1171 through 1181 removed outlier: 3.726A pdb=" N GLU B1176 " --> pdb=" O PRO B1172 " (cutoff:3.500A) Proline residue: B1179 - end of helix Processing helix chain 'B' and resid 1204 through 1219 Processing helix chain 'C' and resid 110 through 123 removed outlier: 3.977A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.618A pdb=" N ARG C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.512A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 321 through 336 removed outlier: 3.822A pdb=" N THR C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 368 through 386 removed outlier: 6.846A pdb=" N HIS C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 409 through 412 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.645A pdb=" N LEU C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 503 Processing helix chain 'C' and resid 508 through 510 No H-bonds generated for 'chain 'C' and resid 508 through 510' Processing helix chain 'C' and resid 516 through 532 Proline residue: C 520 - end of helix removed outlier: 3.795A pdb=" N ASP C 523 " --> pdb=" O PRO C 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 525 " --> pdb=" O MET C 522 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 526 " --> pdb=" O ASP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 552 Processing helix chain 'C' and resid 558 through 561 No H-bonds generated for 'chain 'C' and resid 558 through 561' Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 645 through 650 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.132A pdb=" N LEU C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 688 No H-bonds generated for 'chain 'C' and resid 686 through 688' Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 714 through 731 removed outlier: 3.513A pdb=" N ARG C 729 " --> pdb=" O THR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 770 through 778 Processing helix chain 'C' and resid 786 through 803 removed outlier: 3.567A pdb=" N ALA C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS C 797 " --> pdb=" O VAL C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 847 removed outlier: 3.566A pdb=" N ALA C 846 " --> pdb=" O GLU C 842 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 873 removed outlier: 4.224A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 926 through 933 Processing helix chain 'C' and resid 950 through 962 removed outlier: 3.508A pdb=" N GLU C 956 " --> pdb=" O GLY C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 987 removed outlier: 4.266A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 982 " --> pdb=" O ASN C 979 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR C 983 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP C 986 " --> pdb=" O THR C 983 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 987 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 Processing helix chain 'C' and resid 1022 through 1028 removed outlier: 3.677A pdb=" N LEU C1028 " --> pdb=" O ARG C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1054 Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1079 through 1082 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1112 through 1124 removed outlier: 3.642A pdb=" N ALA C1118 " --> pdb=" O TYR C1115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C1124 " --> pdb=" O LYS C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1150 Processing helix chain 'C' and resid 1171 through 1181 removed outlier: 3.728A pdb=" N GLU C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) Proline residue: C1179 - end of helix Processing helix chain 'C' and resid 1204 through 1219 Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.977A pdb=" N LEU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.619A pdb=" N ARG D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.514A pdb=" N ILE D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 321 through 336 removed outlier: 3.823A pdb=" N THR D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 368 through 386 removed outlier: 6.842A pdb=" N HIS D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE D 386 " --> pdb=" O ARG D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 409 through 412 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 461 through 473 removed outlier: 3.647A pdb=" N LEU D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 503 Processing helix chain 'D' and resid 508 through 510 No H-bonds generated for 'chain 'D' and resid 508 through 510' Processing helix chain 'D' and resid 516 through 532 Proline residue: D 520 - end of helix removed outlier: 3.795A pdb=" N ASP D 523 " --> pdb=" O PRO D 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 525 " --> pdb=" O MET D 522 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 552 Processing helix chain 'D' and resid 558 through 561 No H-bonds generated for 'chain 'D' and resid 558 through 561' Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 645 through 650 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.135A pdb=" N LEU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 688 No H-bonds generated for 'chain 'D' and resid 686 through 688' Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'D' and resid 714 through 731 removed outlier: 3.513A pdb=" N ARG D 729 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' Processing helix chain 'D' and resid 760 through 764 Processing helix chain 'D' and resid 770 through 778 Processing helix chain 'D' and resid 786 through 803 removed outlier: 3.567A pdb=" N ALA D 791 " --> pdb=" O GLU D 787 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 792 " --> pdb=" O ASP D 788 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS D 797 " --> pdb=" O VAL D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 847 removed outlier: 3.565A pdb=" N ALA D 846 " --> pdb=" O GLU D 842 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 873 removed outlier: 4.227A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 926 through 933 Processing helix chain 'D' and resid 950 through 962 removed outlier: 3.509A pdb=" N GLU D 956 " --> pdb=" O GLY D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 987 removed outlier: 4.266A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 982 " --> pdb=" O ASN D 979 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N THR D 983 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 986 " --> pdb=" O THR D 983 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D 987 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 Processing helix chain 'D' and resid 1022 through 1028 removed outlier: 3.678A pdb=" N LEU D1028 " --> pdb=" O ARG D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1054 Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1079 through 1082 Processing helix chain 'D' and resid 1100 through 1102 No H-bonds generated for 'chain 'D' and resid 1100 through 1102' Processing helix chain 'D' and resid 1112 through 1124 removed outlier: 3.642A pdb=" N ALA D1118 " --> pdb=" O TYR D1115 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D1124 " --> pdb=" O LYS D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1150 Processing helix chain 'D' and resid 1171 through 1181 removed outlier: 3.727A pdb=" N GLU D1176 " --> pdb=" O PRO D1172 " (cutoff:3.500A) Proline residue: D1179 - end of helix Processing helix chain 'D' and resid 1204 through 1219 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.975A pdb=" N LEU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.618A pdb=" N ARG E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.514A pdb=" N ILE E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 250 No H-bonds generated for 'chain 'E' and resid 248 through 250' Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 321 through 336 removed outlier: 3.824A pdb=" N THR E 336 " --> pdb=" O SER E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 368 through 386 removed outlier: 6.841A pdb=" N HIS E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE E 386 " --> pdb=" O ARG E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 409 through 412 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 428 through 430 No H-bonds generated for 'chain 'E' and resid 428 through 430' Processing helix chain 'E' and resid 436 through 447 Processing helix chain 'E' and resid 461 through 473 removed outlier: 3.646A pdb=" N LEU E 467 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 503 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 516 through 532 Proline residue: E 520 - end of helix removed outlier: 3.795A pdb=" N ASP E 523 " --> pdb=" O PRO E 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 525 " --> pdb=" O MET E 522 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 526 " --> pdb=" O ASP E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 558 through 561 No H-bonds generated for 'chain 'E' and resid 558 through 561' Processing helix chain 'E' and resid 614 through 628 Processing helix chain 'E' and resid 645 through 650 Processing helix chain 'E' and resid 653 through 660 removed outlier: 4.132A pdb=" N LEU E 660 " --> pdb=" O GLU E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 688 No H-bonds generated for 'chain 'E' and resid 686 through 688' Processing helix chain 'E' and resid 697 through 702 Processing helix chain 'E' and resid 714 through 731 removed outlier: 3.514A pdb=" N ARG E 729 " --> pdb=" O THR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 755 No H-bonds generated for 'chain 'E' and resid 753 through 755' Processing helix chain 'E' and resid 760 through 764 Processing helix chain 'E' and resid 770 through 778 Processing helix chain 'E' and resid 786 through 803 removed outlier: 3.567A pdb=" N ALA E 791 " --> pdb=" O GLU E 787 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 792 " --> pdb=" O ASP E 788 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE E 796 " --> pdb=" O VAL E 792 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS E 797 " --> pdb=" O VAL E 793 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 3.565A pdb=" N ALA E 846 " --> pdb=" O GLU E 842 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE E 847 " --> pdb=" O LEU E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 873 removed outlier: 4.224A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR E 872 " --> pdb=" O VAL E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 892 Processing helix chain 'E' and resid 926 through 933 Processing helix chain 'E' and resid 950 through 962 removed outlier: 3.509A pdb=" N GLU E 956 " --> pdb=" O GLY E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 987 removed outlier: 4.267A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN E 982 " --> pdb=" O ASN E 979 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR E 983 " --> pdb=" O GLY E 980 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP E 986 " --> pdb=" O THR E 983 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU E 987 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 996 Processing helix chain 'E' and resid 1022 through 1028 removed outlier: 3.676A pdb=" N LEU E1028 " --> pdb=" O ARG E1024 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1069 through 1071 No H-bonds generated for 'chain 'E' and resid 1069 through 1071' Processing helix chain 'E' and resid 1079 through 1082 Processing helix chain 'E' and resid 1100 through 1102 No H-bonds generated for 'chain 'E' and resid 1100 through 1102' Processing helix chain 'E' and resid 1112 through 1124 removed outlier: 3.642A pdb=" N ALA E1118 " --> pdb=" O TYR E1115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP E1124 " --> pdb=" O LYS E1121 " (cutoff:3.500A) Processing helix chain 'E' and resid 1142 through 1150 Processing helix chain 'E' and resid 1171 through 1181 removed outlier: 3.729A pdb=" N GLU E1176 " --> pdb=" O PRO E1172 " (cutoff:3.500A) Proline residue: E1179 - end of helix Processing helix chain 'E' and resid 1204 through 1219 Processing helix chain 'F' and resid 110 through 123 removed outlier: 3.979A pdb=" N LEU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.622A pdb=" N ARG F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 175 through 178 Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 226 through 241 removed outlier: 3.514A pdb=" N ILE F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 296 through 302 Processing helix chain 'F' and resid 321 through 336 removed outlier: 3.823A pdb=" N THR F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 368 through 386 removed outlier: 6.848A pdb=" N HIS F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE F 386 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 409 through 412 Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 461 through 473 removed outlier: 3.646A pdb=" N LEU F 467 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 503 Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 516 through 532 Proline residue: F 520 - end of helix removed outlier: 3.795A pdb=" N ASP F 523 " --> pdb=" O PRO F 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 525 " --> pdb=" O MET F 522 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE F 526 " --> pdb=" O ASP F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 552 Processing helix chain 'F' and resid 558 through 561 No H-bonds generated for 'chain 'F' and resid 558 through 561' Processing helix chain 'F' and resid 614 through 628 Processing helix chain 'F' and resid 645 through 650 Processing helix chain 'F' and resid 653 through 660 removed outlier: 4.133A pdb=" N LEU F 660 " --> pdb=" O GLU F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 697 through 702 Processing helix chain 'F' and resid 714 through 731 removed outlier: 3.513A pdb=" N ARG F 729 " --> pdb=" O THR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 755 No H-bonds generated for 'chain 'F' and resid 753 through 755' Processing helix chain 'F' and resid 760 through 764 Processing helix chain 'F' and resid 770 through 778 Processing helix chain 'F' and resid 786 through 803 removed outlier: 3.570A pdb=" N ALA F 791 " --> pdb=" O GLU F 787 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 792 " --> pdb=" O ASP F 788 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE F 796 " --> pdb=" O VAL F 792 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS F 797 " --> pdb=" O VAL F 793 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 847 removed outlier: 3.563A pdb=" N ALA F 846 " --> pdb=" O GLU F 842 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE F 847 " --> pdb=" O LEU F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 873 removed outlier: 4.221A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 892 Processing helix chain 'F' and resid 926 through 933 Processing helix chain 'F' and resid 950 through 962 removed outlier: 3.507A pdb=" N GLU F 956 " --> pdb=" O GLY F 952 " (cutoff:3.500A) Processing helix chain 'F' and resid 975 through 987 removed outlier: 4.264A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 982 " --> pdb=" O ASN F 979 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR F 983 " --> pdb=" O GLY F 980 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP F 986 " --> pdb=" O THR F 983 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU F 987 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 992 through 996 Processing helix chain 'F' and resid 1022 through 1028 removed outlier: 3.677A pdb=" N LEU F1028 " --> pdb=" O ARG F1024 " (cutoff:3.500A) Processing helix chain 'F' and resid 1042 through 1054 Processing helix chain 'F' and resid 1069 through 1071 No H-bonds generated for 'chain 'F' and resid 1069 through 1071' Processing helix chain 'F' and resid 1079 through 1082 Processing helix chain 'F' and resid 1100 through 1102 No H-bonds generated for 'chain 'F' and resid 1100 through 1102' Processing helix chain 'F' and resid 1112 through 1124 removed outlier: 3.641A pdb=" N ALA F1118 " --> pdb=" O TYR F1115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP F1124 " --> pdb=" O LYS F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1142 through 1150 Processing helix chain 'F' and resid 1171 through 1181 removed outlier: 3.727A pdb=" N GLU F1176 " --> pdb=" O PRO F1172 " (cutoff:3.500A) Proline residue: F1179 - end of helix Processing helix chain 'F' and resid 1204 through 1219 Processing sheet with id= A, first strand: chain 'A' and resid 126 through 134 removed outlier: 6.536A pdb=" N SER A 256 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL A 282 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A 258 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 201 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 204 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 212 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= C, first strand: chain 'A' and resid 422 through 424 Processing sheet with id= D, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.781A pdb=" N PHE A 736 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL A 709 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 738 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A 672 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 674 " --> pdb=" O PRO A 639 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 641 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 676 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS A 643 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N VAL A 537 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A 600 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE A 539 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 602 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.608A pdb=" N GLY A 900 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 967 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA A 899 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 969 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A1003 " --> pdb=" O TRP A 970 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A1061 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU A1006 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A1063 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A1037 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1129 through 1133 removed outlier: 6.864A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU A1157 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU A1108 " --> pdb=" O GLU A1157 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A1159 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 126 through 134 removed outlier: 6.535A pdb=" N SER B 256 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL B 282 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 258 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 201 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 204 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 212 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 180 through 184 Processing sheet with id= I, first strand: chain 'B' and resid 422 through 424 Processing sheet with id= J, first strand: chain 'B' and resid 451 through 454 removed outlier: 6.783A pdb=" N PHE B 736 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL B 709 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 738 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ILE B 672 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE B 674 " --> pdb=" O PRO B 639 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 641 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL B 676 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS B 643 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL B 537 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS B 600 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 539 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER B 602 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 939 through 944 removed outlier: 3.608A pdb=" N GLY B 900 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 967 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA B 899 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 969 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B1003 " --> pdb=" O TRP B 970 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B1061 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU B1006 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B1063 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B1037 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1129 through 1133 removed outlier: 6.867A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B1157 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU B1108 " --> pdb=" O GLU B1157 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B1159 " --> pdb=" O LEU B1108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 126 through 134 removed outlier: 6.540A pdb=" N SER C 256 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL C 282 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C 258 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 201 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 204 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 212 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 184 Processing sheet with id= O, first strand: chain 'C' and resid 422 through 424 Processing sheet with id= P, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.782A pdb=" N PHE C 736 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL C 709 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP C 738 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ILE C 672 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE C 674 " --> pdb=" O PRO C 639 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU C 641 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 676 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N HIS C 643 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL C 537 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS C 600 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE C 539 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER C 602 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 939 through 944 removed outlier: 3.609A pdb=" N GLY C 900 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 967 " --> pdb=" O ARG C 897 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA C 899 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 969 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C1003 " --> pdb=" O TRP C 970 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C1061 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU C1006 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C1063 " --> pdb=" O LEU C1006 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA C1037 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1129 through 1133 removed outlier: 6.864A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU C1157 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C1108 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU C1159 " --> pdb=" O LEU C1108 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 126 through 134 removed outlier: 6.533A pdb=" N SER D 256 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL D 282 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR D 258 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA D 201 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 204 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 212 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 180 through 184 Processing sheet with id= U, first strand: chain 'D' and resid 422 through 424 Processing sheet with id= V, first strand: chain 'D' and resid 451 through 454 removed outlier: 6.782A pdb=" N PHE D 736 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL D 709 " --> pdb=" O PHE D 736 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP D 738 " --> pdb=" O VAL D 709 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ILE D 672 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 674 " --> pdb=" O PRO D 639 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 641 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL D 676 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N HIS D 643 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N VAL D 537 " --> pdb=" O GLU D 598 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS D 600 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE D 539 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER D 602 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 939 through 944 removed outlier: 3.607A pdb=" N GLY D 900 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 967 " --> pdb=" O ARG D 897 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ALA D 899 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 969 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D1003 " --> pdb=" O TRP D 970 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D1061 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU D1006 " --> pdb=" O LEU D1061 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D1063 " --> pdb=" O LEU D1006 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA D1037 " --> pdb=" O PHE D1064 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1129 through 1133 removed outlier: 6.866A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU D1157 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU D1108 " --> pdb=" O GLU D1157 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D1159 " --> pdb=" O LEU D1108 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 126 through 134 removed outlier: 6.533A pdb=" N SER E 256 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL E 282 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR E 258 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 201 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 204 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 212 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 180 through 184 Processing sheet with id= AA, first strand: chain 'E' and resid 422 through 424 Processing sheet with id= AB, first strand: chain 'E' and resid 451 through 454 removed outlier: 6.779A pdb=" N PHE E 736 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL E 709 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP E 738 " --> pdb=" O VAL E 709 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ILE E 672 " --> pdb=" O VAL E 637 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE E 674 " --> pdb=" O PRO E 639 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU E 641 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL E 676 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N HIS E 643 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N VAL E 537 " --> pdb=" O GLU E 598 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS E 600 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE E 539 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER E 602 " --> pdb=" O ILE E 539 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 939 through 944 removed outlier: 3.608A pdb=" N GLY E 900 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE E 967 " --> pdb=" O ARG E 897 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ALA E 899 " --> pdb=" O ILE E 967 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA E 969 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E1003 " --> pdb=" O TRP E 970 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU E1061 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU E1006 " --> pdb=" O LEU E1061 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E1063 " --> pdb=" O LEU E1006 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA E1037 " --> pdb=" O PHE E1064 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 1129 through 1133 removed outlier: 6.864A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU E1157 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU E1108 " --> pdb=" O GLU E1157 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU E1159 " --> pdb=" O LEU E1108 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 126 through 134 removed outlier: 6.537A pdb=" N SER F 256 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL F 282 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR F 258 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 201 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU F 204 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 212 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 180 through 184 Processing sheet with id= AG, first strand: chain 'F' and resid 422 through 424 Processing sheet with id= AH, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.780A pdb=" N PHE F 736 " --> pdb=" O PHE F 707 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL F 709 " --> pdb=" O PHE F 736 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP F 738 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ILE F 672 " --> pdb=" O VAL F 637 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE F 674 " --> pdb=" O PRO F 639 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU F 641 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL F 676 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS F 643 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL F 537 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS F 600 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE F 539 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER F 602 " --> pdb=" O ILE F 539 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 939 through 944 removed outlier: 3.608A pdb=" N GLY F 900 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE F 967 " --> pdb=" O ARG F 897 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA F 899 " --> pdb=" O ILE F 967 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA F 969 " --> pdb=" O ALA F 899 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F1003 " --> pdb=" O TRP F 970 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F1061 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU F1006 " --> pdb=" O LEU F1061 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE F1063 " --> pdb=" O LEU F1006 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA F1037 " --> pdb=" O PHE F1064 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 1129 through 1133 removed outlier: 6.858A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU F1157 " --> pdb=" O VAL F1106 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU F1108 " --> pdb=" O GLU F1157 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F1159 " --> pdb=" O LEU F1108 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG G 134 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 67 through 70 Processing sheet with id= AM, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.918A pdb=" N ARG H 134 " --> pdb=" O LYS H 52 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 67 through 70 Processing sheet with id= AO, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG I 134 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 67 through 70 Processing sheet with id= AQ, first strand: chain 'J' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG J 134 " --> pdb=" O LYS J 52 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 67 through 70 Processing sheet with id= AS, first strand: chain 'K' and resid 60 through 63 removed outlier: 6.917A pdb=" N ARG K 134 " --> pdb=" O LYS K 52 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'K' and resid 67 through 70 Processing sheet with id= AU, first strand: chain 'L' and resid 60 through 63 removed outlier: 6.918A pdb=" N ARG L 134 " --> pdb=" O LYS L 52 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 67 through 70 1962 hydrogen bonds defined for protein. 5238 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: 21.48 Time building geometry restraints manager: 16.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10298 1.32 - 1.44: 13840 1.44 - 1.57: 31916 1.57 - 1.69: 24 1.69 - 1.82: 420 Bond restraints: 56498 Sorted by residual: bond pdb=" CA SER D 869 " pdb=" CB SER D 869 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.56e-02 4.11e+03 2.42e+01 bond pdb=" CA SER B 869 " pdb=" CB SER B 869 " ideal model delta sigma weight residual 1.531 1.455 0.077 1.56e-02 4.11e+03 2.41e+01 bond pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.34e+01 bond pdb=" N VAL E 401 " pdb=" CA VAL E 401 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.33e+01 bond pdb=" N VAL A 401 " pdb=" CA VAL A 401 " ideal model delta sigma weight residual 1.460 1.495 -0.036 7.50e-03 1.78e+04 2.25e+01 ... (remaining 56493 not shown) Histogram of bond angle deviations from ideal: 91.31 - 100.86: 233 100.86 - 110.41: 15010 110.41 - 119.96: 39523 119.96 - 129.51: 21501 129.51 - 139.06: 330 Bond angle restraints: 76597 Sorted by residual: angle pdb=" CA GLY D 670 " pdb=" C GLY D 670 " pdb=" O GLY D 670 " ideal model delta sigma weight residual 122.22 118.06 4.16 6.50e-01 2.37e+00 4.10e+01 angle pdb=" CA GLY B 670 " pdb=" C GLY B 670 " pdb=" O GLY B 670 " ideal model delta sigma weight residual 122.22 118.08 4.14 6.50e-01 2.37e+00 4.05e+01 angle pdb=" CA GLY C 670 " pdb=" C GLY C 670 " pdb=" O GLY C 670 " ideal model delta sigma weight residual 122.22 118.13 4.09 6.50e-01 2.37e+00 3.97e+01 angle pdb=" CA GLY E 670 " pdb=" C GLY E 670 " pdb=" O GLY E 670 " ideal model delta sigma weight residual 122.22 118.14 4.08 6.50e-01 2.37e+00 3.93e+01 angle pdb=" CA GLY F 670 " pdb=" C GLY F 670 " pdb=" O GLY F 670 " ideal model delta sigma weight residual 122.22 118.15 4.07 6.50e-01 2.37e+00 3.92e+01 ... (remaining 76592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 30779 17.25 - 34.51: 2321 34.51 - 51.76: 598 51.76 - 69.01: 151 69.01 - 86.27: 42 Dihedral angle restraints: 33891 sinusoidal: 13587 harmonic: 20304 Sorted by residual: dihedral pdb=" CA LYS C 156 " pdb=" C LYS C 156 " pdb=" N ILE C 157 " pdb=" CA ILE C 157 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LYS F 156 " pdb=" C LYS F 156 " pdb=" N ILE F 157 " pdb=" CA ILE F 157 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LYS D 156 " pdb=" C LYS D 156 " pdb=" N ILE D 157 " pdb=" CA ILE D 157 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 33888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4450 0.073 - 0.147: 3077 0.147 - 0.220: 859 0.220 - 0.294: 26 0.294 - 0.367: 18 Chirality restraints: 8430 Sorted by residual: chirality pdb=" CA PRO E 714 " pdb=" N PRO E 714 " pdb=" C PRO E 714 " pdb=" CB PRO E 714 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA PRO C 714 " pdb=" N PRO C 714 " pdb=" C PRO C 714 " pdb=" CB PRO C 714 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA PRO F 714 " pdb=" N PRO F 714 " pdb=" C PRO F 714 " pdb=" CB PRO F 714 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 8427 not shown) Planarity restraints: 10121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2' TPP E1301 " -0.002 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" C4' TPP E1301 " 0.017 2.00e-02 2.50e+03 pdb=" C5' TPP E1301 " 0.027 2.00e-02 2.50e+03 pdb=" C6' TPP E1301 " 0.034 2.00e-02 2.50e+03 pdb=" C7' TPP E1301 " -0.067 2.00e-02 2.50e+03 pdb=" CM2 TPP E1301 " -0.042 2.00e-02 2.50e+03 pdb=" N1' TPP E1301 " 0.018 2.00e-02 2.50e+03 pdb=" N3' TPP E1301 " 0.002 2.00e-02 2.50e+03 pdb=" N4' TPP E1301 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' TPP F1301 " -0.004 2.00e-02 2.50e+03 2.68e-02 1.61e+01 pdb=" C4' TPP F1301 " 0.015 2.00e-02 2.50e+03 pdb=" C5' TPP F1301 " 0.025 2.00e-02 2.50e+03 pdb=" C6' TPP F1301 " 0.029 2.00e-02 2.50e+03 pdb=" C7' TPP F1301 " -0.057 2.00e-02 2.50e+03 pdb=" CM2 TPP F1301 " -0.034 2.00e-02 2.50e+03 pdb=" N1' TPP F1301 " 0.013 2.00e-02 2.50e+03 pdb=" N3' TPP F1301 " 0.001 2.00e-02 2.50e+03 pdb=" N4' TPP F1301 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' TPP A1301 " -0.004 2.00e-02 2.50e+03 2.64e-02 1.57e+01 pdb=" C4' TPP A1301 " 0.014 2.00e-02 2.50e+03 pdb=" C5' TPP A1301 " 0.024 2.00e-02 2.50e+03 pdb=" C6' TPP A1301 " 0.029 2.00e-02 2.50e+03 pdb=" C7' TPP A1301 " -0.057 2.00e-02 2.50e+03 pdb=" CM2 TPP A1301 " -0.032 2.00e-02 2.50e+03 pdb=" N1' TPP A1301 " 0.014 2.00e-02 2.50e+03 pdb=" N3' TPP A1301 " -0.002 2.00e-02 2.50e+03 pdb=" N4' TPP A1301 " 0.014 2.00e-02 2.50e+03 ... (remaining 10118 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6033 2.78 - 3.31: 51137 3.31 - 3.84: 79494 3.84 - 4.37: 112211 4.37 - 4.90: 177797 Nonbonded interactions: 426672 Sorted by model distance: nonbonded pdb=" OD1 ASN B 678 " pdb="MG MG B1302 " model vdw 2.250 2.170 nonbonded pdb=" OD1 ASN D 678 " pdb="MG MG D1302 " model vdw 2.253 2.170 nonbonded pdb=" OD1 ASN F 678 " pdb="MG MG F1302 " model vdw 2.283 2.170 nonbonded pdb=" OD1 ASN C 678 " pdb="MG MG C1301 " model vdw 2.295 2.170 nonbonded pdb=" OD1 ASN A 678 " pdb="MG MG A1302 " model vdw 2.297 2.170 ... (remaining 426667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'B' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'C' and resid 102 through 1221) selection = (chain 'D' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'E' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) selection = (chain 'F' and (resid 102 through 205 or (resid 206 through 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 1221)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 12.900 Check model and map are aligned: 0.600 Set scattering table: 0.500 Process input model: 115.190 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.300 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:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.013 0.077 56498 Z= 0.869 Angle : 1.762 7.807 76597 Z= 1.303 Chirality : 0.091 0.367 8430 Planarity : 0.005 0.033 10121 Dihedral : 14.153 86.268 20871 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.21 % Allowed : 3.60 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -1.93 (0.08), residues: 7062 helix: -1.45 (0.08), residues: 2562 sheet: -0.06 (0.14), residues: 1116 loop : -1.50 (0.09), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP C 417 HIS 0.016 0.004 HIS D 643 PHE 0.030 0.004 PHE F1082 TYR 0.046 0.006 TYR C 856 ARG 0.013 0.001 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1256 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8781 (mmt) cc_final: 0.8029 (mmt) REVERT: A 156 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8616 (mtpm) REVERT: A 257 LEU cc_start: 0.9197 (tp) cc_final: 0.8994 (tt) REVERT: A 290 GLU cc_start: 0.8634 (pm20) cc_final: 0.8347 (pm20) REVERT: A 296 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 405 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8291 (mtm180) REVERT: A 617 MET cc_start: 0.8670 (ttp) cc_final: 0.8455 (tmt) REVERT: A 760 MET cc_start: 0.8774 (ttp) cc_final: 0.8552 (ttp) REVERT: A 787 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 902 ASP cc_start: 0.8057 (m-30) cc_final: 0.7754 (m-30) REVERT: A 905 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8479 (ttp80) REVERT: A 909 THR cc_start: 0.8689 (m) cc_final: 0.8477 (m) REVERT: B 235 ASP cc_start: 0.8460 (t70) cc_final: 0.8184 (t0) REVERT: B 290 GLU cc_start: 0.8648 (pm20) cc_final: 0.8349 (pm20) REVERT: B 296 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 405 ARG cc_start: 0.8677 (mtm180) cc_final: 0.8366 (mtm180) REVERT: B 617 MET cc_start: 0.8772 (ttp) cc_final: 0.8545 (tmt) REVERT: B 692 MET cc_start: 0.9113 (mtm) cc_final: 0.8807 (mtp) REVERT: B 787 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8327 (mt-10) REVERT: B 902 ASP cc_start: 0.8099 (m-30) cc_final: 0.7839 (m-30) REVERT: C 227 SER cc_start: 0.8856 (t) cc_final: 0.8632 (p) REVERT: C 405 ARG cc_start: 0.8533 (mtm180) cc_final: 0.8150 (mtm180) REVERT: C 593 MET cc_start: 0.9197 (tpt) cc_final: 0.8991 (tpt) REVERT: C 617 MET cc_start: 0.8650 (ttp) cc_final: 0.8350 (tmt) REVERT: C 692 MET cc_start: 0.9044 (mtm) cc_final: 0.8820 (mtm) REVERT: C 761 TYR cc_start: 0.8875 (m-80) cc_final: 0.8510 (m-80) REVERT: C 902 ASP cc_start: 0.8000 (m-30) cc_final: 0.7703 (m-30) REVERT: C 905 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8490 (ttp80) REVERT: D 227 SER cc_start: 0.8682 (t) cc_final: 0.8435 (p) REVERT: D 579 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7065 (t70) REVERT: D 593 MET cc_start: 0.9213 (tpt) cc_final: 0.8985 (tpt) REVERT: D 606 ASN cc_start: 0.8839 (p0) cc_final: 0.8617 (p0) REVERT: D 617 MET cc_start: 0.8731 (ttp) cc_final: 0.8491 (tmt) REVERT: D 902 ASP cc_start: 0.8077 (m-30) cc_final: 0.7827 (m-30) REVERT: E 118 MET cc_start: 0.8753 (mmt) cc_final: 0.7785 (mmt) REVERT: E 132 ASP cc_start: 0.8554 (p0) cc_final: 0.8304 (p0) REVERT: E 593 MET cc_start: 0.9228 (tpt) cc_final: 0.8939 (tpt) REVERT: E 617 MET cc_start: 0.8607 (ttp) cc_final: 0.8384 (tmt) REVERT: E 761 TYR cc_start: 0.8837 (m-80) cc_final: 0.8619 (m-80) REVERT: E 902 ASP cc_start: 0.7996 (m-30) cc_final: 0.7746 (m-30) REVERT: E 909 THR cc_start: 0.8649 (m) cc_final: 0.8445 (m) REVERT: F 167 MET cc_start: 0.8755 (ttt) cc_final: 0.8313 (ttt) REVERT: F 405 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8119 (mtm180) REVERT: F 593 MET cc_start: 0.9147 (tpt) cc_final: 0.8933 (tpt) REVERT: F 859 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8450 (ttm170) REVERT: F 902 ASP cc_start: 0.8121 (m-30) cc_final: 0.7852 (m-30) outliers start: 12 outliers final: 2 residues processed: 1268 average time/residue: 1.6558 time to fit residues: 2551.0582 Evaluate side-chains 1127 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1124 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 263 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 0.9980 chunk 536 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 361 optimal weight: 4.9990 chunk 286 optimal weight: 0.8980 chunk 554 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 337 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 642 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 590 HIS A 973 GLN B 117 ASN B 276 GLN B 404 HIS B 498 ASN B 589 GLN B 590 HIS B 973 GLN B1027 GLN B1213 GLN C 251 GLN C 276 GLN C 973 GLN D 276 GLN D 292 GLN D 316 HIS D 320 GLN D 498 ASN D1027 GLN D1045 HIS E 251 GLN E 276 GLN E 320 GLN E 498 ASN E 973 GLN F 276 GLN F 359 GLN F 590 HIS F 973 GLN F1027 GLN F1045 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 56498 Z= 0.171 Angle : 0.529 5.650 76597 Z= 0.280 Chirality : 0.043 0.163 8430 Planarity : 0.004 0.050 10121 Dihedral : 4.960 59.238 7758 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.39 % Allowed : 9.02 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.14 (0.09), residues: 7062 helix: 0.71 (0.10), residues: 2586 sheet: 0.32 (0.14), residues: 1344 loop : -0.90 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 466 HIS 0.004 0.001 HIS F 267 PHE 0.021 0.001 PHE F1046 TYR 0.015 0.001 TYR D 761 ARG 0.007 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1216 time to evaluate : 4.758 Fit side-chains REVERT: A 290 GLU cc_start: 0.8554 (pm20) cc_final: 0.8257 (pm20) REVERT: A 296 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8358 (mm-30) REVERT: A 902 ASP cc_start: 0.8095 (m-30) cc_final: 0.7802 (m-30) REVERT: A 909 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 1208 GLN cc_start: 0.8517 (mt0) cc_final: 0.8297 (mt0) REVERT: B 290 GLU cc_start: 0.8536 (pm20) cc_final: 0.8264 (pm20) REVERT: B 296 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8301 (mm-30) REVERT: B 405 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8410 (mtm180) REVERT: B 902 ASP cc_start: 0.8114 (m-30) cc_final: 0.7855 (m-30) REVERT: C 152 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 167 MET cc_start: 0.8689 (ttt) cc_final: 0.8450 (ttt) REVERT: C 405 ARG cc_start: 0.8500 (mtm180) cc_final: 0.8166 (mtm180) REVERT: C 761 TYR cc_start: 0.8735 (m-80) cc_final: 0.8455 (m-80) REVERT: C 902 ASP cc_start: 0.8023 (m-30) cc_final: 0.7737 (m-30) REVERT: D 286 ASP cc_start: 0.8574 (t0) cc_final: 0.8317 (t0) REVERT: D 579 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6952 (t70) REVERT: D 902 ASP cc_start: 0.8103 (m-30) cc_final: 0.7898 (m-30) REVERT: E 434 MET cc_start: 0.8841 (ttm) cc_final: 0.8622 (ttm) REVERT: E 761 TYR cc_start: 0.8684 (m-80) cc_final: 0.8214 (m-80) REVERT: E 902 ASP cc_start: 0.8053 (m-30) cc_final: 0.7827 (m-30) REVERT: E 949 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: F 152 THR cc_start: 0.8788 (m) cc_final: 0.8543 (p) REVERT: F 185 ASP cc_start: 0.8291 (t0) cc_final: 0.8015 (t0) REVERT: F 257 LEU cc_start: 0.9028 (tp) cc_final: 0.8796 (tp) REVERT: F 405 ARG cc_start: 0.8552 (mtm180) cc_final: 0.8176 (mtm180) REVERT: F 763 LEU cc_start: 0.8663 (mt) cc_final: 0.8451 (mt) REVERT: F 859 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8491 (ttm170) REVERT: F 902 ASP cc_start: 0.8128 (m-30) cc_final: 0.7903 (m-30) REVERT: F 1027 GLN cc_start: 0.8432 (tt0) cc_final: 0.8222 (tt0) REVERT: I 46 SER cc_start: 0.8733 (p) cc_final: 0.8529 (p) REVERT: I 72 ARG cc_start: 0.8982 (ttt180) cc_final: 0.8704 (ttt-90) REVERT: L 46 SER cc_start: 0.8747 (p) cc_final: 0.8544 (p) outliers start: 81 outliers final: 15 residues processed: 1233 average time/residue: 1.6967 time to fit residues: 2539.8311 Evaluate side-chains 1180 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1161 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1199 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 700 LYS Chi-restraints excluded: chain E residue 949 GLU Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain F residue 1163 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 0.0980 chunk 199 optimal weight: 0.9990 chunk 535 optimal weight: 0.6980 chunk 437 optimal weight: 8.9990 chunk 177 optimal weight: 0.0980 chunk 644 optimal weight: 1.9990 chunk 695 optimal weight: 0.8980 chunk 573 optimal weight: 1.9990 chunk 638 optimal weight: 0.0970 chunk 219 optimal weight: 3.9990 chunk 516 optimal weight: 0.4980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A 677 ASN A 973 GLN B 404 HIS B 677 ASN C 251 GLN C 677 ASN C 944 ASN D 292 GLN D 320 GLN D 677 ASN D1045 HIS E 251 GLN E 363 ASN E 677 ASN E 944 ASN E 973 GLN F 677 ASN F 944 ASN F1138 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 56498 Z= 0.106 Angle : 0.440 7.002 76597 Z= 0.227 Chirality : 0.041 0.135 8430 Planarity : 0.004 0.042 10121 Dihedral : 4.197 56.290 7756 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.13 % Allowed : 11.18 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.56 (0.10), residues: 7062 helix: 1.25 (0.10), residues: 2652 sheet: 0.74 (0.14), residues: 1410 loop : -0.57 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 466 HIS 0.003 0.000 HIS B1177 PHE 0.019 0.001 PHE D1046 TYR 0.014 0.001 TYR D 233 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1250 time to evaluate : 4.618 Fit side-chains REVERT: A 290 GLU cc_start: 0.8562 (pm20) cc_final: 0.8273 (pm20) REVERT: A 1208 GLN cc_start: 0.8394 (mt0) cc_final: 0.8192 (mt0) REVERT: B 290 GLU cc_start: 0.8530 (pm20) cc_final: 0.8250 (pm20) REVERT: B 296 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8284 (mm-30) REVERT: B 405 ARG cc_start: 0.8604 (mtm180) cc_final: 0.8382 (mtm180) REVERT: B 902 ASP cc_start: 0.8062 (m-30) cc_final: 0.7808 (m-30) REVERT: C 152 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8506 (p) REVERT: C 405 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8226 (mtm180) REVERT: C 761 TYR cc_start: 0.8538 (m-80) cc_final: 0.8220 (m-80) REVERT: C 902 ASP cc_start: 0.7956 (m-30) cc_final: 0.7667 (m-30) REVERT: D 579 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6875 (t70) REVERT: D 1071 ARG cc_start: 0.8823 (mtt90) cc_final: 0.8529 (mtt180) REVERT: E 167 MET cc_start: 0.8731 (ttt) cc_final: 0.8527 (ttt) REVERT: E 248 ASP cc_start: 0.8579 (m-30) cc_final: 0.8345 (t0) REVERT: E 761 TYR cc_start: 0.8396 (m-80) cc_final: 0.7960 (m-80) REVERT: F 185 ASP cc_start: 0.8206 (t0) cc_final: 0.7879 (t0) REVERT: F 257 LEU cc_start: 0.8957 (tp) cc_final: 0.8729 (tp) REVERT: F 405 ARG cc_start: 0.8527 (mtm180) cc_final: 0.8190 (mtm180) REVERT: F 788 ASP cc_start: 0.8208 (m-30) cc_final: 0.8005 (m-30) REVERT: F 859 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8489 (ttm170) REVERT: F 1185 MET cc_start: 0.8925 (ttp) cc_final: 0.8585 (ttm) REVERT: I 72 ARG cc_start: 0.8897 (ttt180) cc_final: 0.8648 (ttt-90) outliers start: 66 outliers final: 17 residues processed: 1272 average time/residue: 1.6138 time to fit residues: 2513.2278 Evaluate side-chains 1218 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1199 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 1123 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 248 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 5.9990 chunk 484 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 432 optimal weight: 1.9990 chunk 646 optimal weight: 3.9990 chunk 684 optimal weight: 5.9990 chunk 337 optimal weight: 0.7980 chunk 612 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN A 677 ASN B 404 HIS B 677 ASN B 679 GLN B 973 GLN C 251 GLN C 679 GLN C 944 ASN D 363 ASN D 677 ASN D 679 GLN D 936 ASN E 251 GLN E 677 ASN E 944 ASN E1167 ASN E1184 ASN F 363 ASN F 677 ASN F 679 GLN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 56498 Z= 0.201 Angle : 0.479 7.543 76597 Z= 0.250 Chirality : 0.043 0.147 8430 Planarity : 0.004 0.036 10121 Dihedral : 4.260 59.545 7756 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.23 % Allowed : 12.57 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.79 (0.10), residues: 7062 helix: 1.52 (0.10), residues: 2598 sheet: 0.88 (0.14), residues: 1404 loop : -0.49 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 466 HIS 0.005 0.001 HIS F 267 PHE 0.025 0.001 PHE F1046 TYR 0.015 0.001 TYR D 233 ARG 0.008 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1215 time to evaluate : 4.636 Fit side-chains REVERT: A 144 MET cc_start: 0.8323 (mtp) cc_final: 0.8111 (mtm) REVERT: A 290 GLU cc_start: 0.8603 (pm20) cc_final: 0.8292 (pm20) REVERT: A 1059 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8427 (mtt90) REVERT: A 1208 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: B 290 GLU cc_start: 0.8577 (pm20) cc_final: 0.8271 (pm20) REVERT: B 296 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8262 (mm-30) REVERT: B 405 ARG cc_start: 0.8594 (mtm180) cc_final: 0.8359 (mtm180) REVERT: B 902 ASP cc_start: 0.8084 (m-30) cc_final: 0.7842 (m-30) REVERT: B 1059 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8414 (mtt90) REVERT: B 1208 GLN cc_start: 0.8626 (mt0) cc_final: 0.8365 (mt0) REVERT: C 152 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8508 (p) REVERT: C 501 GLN cc_start: 0.8344 (tp40) cc_final: 0.8107 (mp10) REVERT: C 902 ASP cc_start: 0.8014 (m-30) cc_final: 0.7748 (m-30) REVERT: D 579 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6835 (t70) REVERT: E 248 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8340 (t0) REVERT: E 761 TYR cc_start: 0.8495 (m-80) cc_final: 0.8169 (m-80) REVERT: E 949 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: E 1208 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: F 185 ASP cc_start: 0.8262 (t0) cc_final: 0.7964 (t0) REVERT: F 257 LEU cc_start: 0.8971 (tp) cc_final: 0.8753 (tp) REVERT: F 405 ARG cc_start: 0.8505 (mtm180) cc_final: 0.8173 (mtm180) REVERT: F 593 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.7551 (tpt) REVERT: F 859 ARG cc_start: 0.8690 (ttm170) cc_final: 0.8470 (ttm170) REVERT: I 72 ARG cc_start: 0.8995 (ttt180) cc_final: 0.8771 (ttt-90) outliers start: 72 outliers final: 26 residues processed: 1232 average time/residue: 1.6803 time to fit residues: 2519.2294 Evaluate side-chains 1237 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1202 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 837 ARG Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1199 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 949 GLU Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain E residue 1208 GLN Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 947 LEU Chi-restraints excluded: chain F residue 1123 LYS Chi-restraints excluded: chain F residue 1209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 509 optimal weight: 6.9990 chunk 282 optimal weight: 0.6980 chunk 583 optimal weight: 2.9990 chunk 473 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 614 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 799 GLN B 404 HIS B 677 ASN B 679 GLN C 251 GLN C 363 ASN C 944 ASN D 292 GLN D 677 ASN D 679 GLN ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 GLN E 320 GLN E 677 ASN E 944 ASN E 973 GLN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 677 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 56498 Z= 0.257 Angle : 0.495 7.568 76597 Z= 0.260 Chirality : 0.044 0.153 8430 Planarity : 0.004 0.040 10121 Dihedral : 4.326 51.712 7756 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.39 % Allowed : 12.88 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.69 (0.10), residues: 7062 helix: 1.44 (0.10), residues: 2598 sheet: 0.97 (0.14), residues: 1302 loop : -0.57 (0.10), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 466 HIS 0.006 0.001 HIS B 643 PHE 0.027 0.002 PHE F1046 TYR 0.016 0.001 TYR D 233 ARG 0.009 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1240 time to evaluate : 4.649 Fit side-chains REVERT: A 290 GLU cc_start: 0.8624 (pm20) cc_final: 0.8293 (pm20) REVERT: A 1059 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8401 (mtt90) REVERT: A 1208 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: B 290 GLU cc_start: 0.8612 (pm20) cc_final: 0.8346 (pm20) REVERT: B 296 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 405 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8306 (mtm180) REVERT: B 902 ASP cc_start: 0.8115 (m-30) cc_final: 0.7897 (m-30) REVERT: B 1059 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8419 (mtt90) REVERT: B 1194 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8364 (ptp90) REVERT: C 152 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 902 ASP cc_start: 0.8020 (m-30) cc_final: 0.7785 (m-30) REVERT: E 248 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8349 (t0) REVERT: E 761 TYR cc_start: 0.8553 (m-80) cc_final: 0.8258 (m-80) REVERT: E 949 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: F 257 LEU cc_start: 0.8973 (tp) cc_final: 0.8754 (tp) REVERT: F 405 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8163 (mtm180) REVERT: F 593 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.7691 (tpt) REVERT: F 859 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8452 (ttm170) REVERT: I 72 ARG cc_start: 0.9010 (ttt180) cc_final: 0.8779 (ttt-90) outliers start: 81 outliers final: 35 residues processed: 1257 average time/residue: 1.6426 time to fit residues: 2520.5035 Evaluate side-chains 1254 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1211 time to evaluate : 6.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1096 ASN Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1123 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 949 GLU Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain F residue 947 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 2.9990 chunk 616 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 685 optimal weight: 6.9990 chunk 568 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 799 GLN B 404 HIS B 677 ASN B 679 GLN C 251 GLN C 363 ASN C 944 ASN D 292 GLN D 677 ASN D 679 GLN ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 GLN E 320 GLN E 677 ASN E 944 ASN ** E 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 ASN F 677 ASN F 722 GLN F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 56498 Z= 0.335 Angle : 0.528 8.091 76597 Z= 0.278 Chirality : 0.046 0.158 8430 Planarity : 0.005 0.041 10121 Dihedral : 4.407 48.290 7754 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.46 % Allowed : 13.29 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.56 (0.10), residues: 7062 helix: 1.30 (0.10), residues: 2604 sheet: 1.02 (0.14), residues: 1254 loop : -0.65 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 466 HIS 0.007 0.001 HIS F 643 PHE 0.030 0.002 PHE F1046 TYR 0.017 0.002 TYR D 233 ARG 0.009 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1235 time to evaluate : 4.682 Fit side-chains REVERT: A 290 GLU cc_start: 0.8644 (pm20) cc_final: 0.8336 (pm20) REVERT: A 1059 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8431 (mtt90) REVERT: A 1208 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8352 (mt0) REVERT: B 405 ARG cc_start: 0.8623 (mtm180) cc_final: 0.8274 (mtm180) REVERT: B 902 ASP cc_start: 0.8130 (m-30) cc_final: 0.7911 (m-30) REVERT: B 1059 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8446 (mtt90) REVERT: B 1194 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (ptp90) REVERT: B 1208 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8408 (mt0) REVERT: C 152 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8536 (p) REVERT: C 501 GLN cc_start: 0.8494 (tp40) cc_final: 0.8230 (mp10) REVERT: C 902 ASP cc_start: 0.8011 (m-30) cc_final: 0.7792 (m-30) REVERT: C 1208 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: D 1208 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: E 248 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8378 (t0) REVERT: E 761 TYR cc_start: 0.8618 (m-80) cc_final: 0.8362 (m-80) REVERT: E 949 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: E 1059 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7908 (mtt90) REVERT: F 257 LEU cc_start: 0.8985 (tp) cc_final: 0.8758 (tp) REVERT: F 405 ARG cc_start: 0.8527 (mtm180) cc_final: 0.8171 (mtm180) REVERT: F 593 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.7715 (tpt) REVERT: F 859 ARG cc_start: 0.8670 (ttm170) cc_final: 0.8443 (ttm170) REVERT: I 72 ARG cc_start: 0.9041 (ttt180) cc_final: 0.8820 (ttt-90) outliers start: 85 outliers final: 42 residues processed: 1258 average time/residue: 1.6818 time to fit residues: 2578.2636 Evaluate side-chains 1276 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1222 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1096 ASN Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain B residue 1208 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 1208 GLN Chi-restraints excluded: chain C residue 1209 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 880 TRP Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1199 THR Chi-restraints excluded: chain D residue 1208 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 949 GLU Chi-restraints excluded: chain E residue 1059 ARG Chi-restraints excluded: chain E residue 1123 LYS Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 614 ASN Chi-restraints excluded: chain F residue 801 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 390 optimal weight: 3.9990 chunk 500 optimal weight: 0.6980 chunk 387 optimal weight: 10.0000 chunk 576 optimal weight: 0.8980 chunk 382 optimal weight: 0.6980 chunk 682 optimal weight: 5.9990 chunk 427 optimal weight: 0.8980 chunk 416 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 799 GLN B 404 HIS B 679 GLN C 944 ASN D 292 GLN D 404 HIS D 677 ASN D 679 GLN D 973 GLN E 251 GLN E 677 ASN E 944 ASN E 973 GLN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 677 ASN F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 56498 Z= 0.220 Angle : 0.475 7.709 76597 Z= 0.249 Chirality : 0.044 0.146 8430 Planarity : 0.004 0.043 10121 Dihedral : 4.192 46.375 7752 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.17 % Allowed : 13.96 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.68 (0.10), residues: 7062 helix: 1.41 (0.10), residues: 2598 sheet: 0.99 (0.14), residues: 1326 loop : -0.57 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 466 HIS 0.005 0.001 HIS F 267 PHE 0.026 0.001 PHE F1046 TYR 0.016 0.001 TYR D 761 ARG 0.009 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1238 time to evaluate : 4.782 Fit side-chains REVERT: A 290 GLU cc_start: 0.8634 (pm20) cc_final: 0.8331 (pm20) REVERT: A 1059 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8369 (mtt90) REVERT: A 1208 GLN cc_start: 0.8550 (mt0) cc_final: 0.8307 (mt0) REVERT: B 290 GLU cc_start: 0.8626 (pm20) cc_final: 0.8358 (pm20) REVERT: B 405 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8257 (mtm180) REVERT: B 902 ASP cc_start: 0.8118 (m-30) cc_final: 0.7911 (m-30) REVERT: B 1059 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (mtt90) REVERT: B 1194 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8381 (ptp90) REVERT: C 152 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 902 ASP cc_start: 0.7992 (m-30) cc_final: 0.7790 (m-30) REVERT: C 1208 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: D 1059 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7890 (mtt90) REVERT: E 248 ASP cc_start: 0.8603 (m-30) cc_final: 0.8382 (t0) REVERT: E 501 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: E 629 ASP cc_start: 0.8435 (t0) cc_final: 0.8172 (t0) REVERT: E 761 TYR cc_start: 0.8526 (m-80) cc_final: 0.8276 (m-80) REVERT: E 947 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8660 (tt) REVERT: F 257 LEU cc_start: 0.8965 (tp) cc_final: 0.8743 (tp) REVERT: F 405 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8179 (mtm180) REVERT: F 593 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.7602 (tpt) REVERT: F 859 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8445 (ttm170) REVERT: I 72 ARG cc_start: 0.8996 (ttt180) cc_final: 0.8772 (ttt-90) outliers start: 68 outliers final: 37 residues processed: 1258 average time/residue: 1.6819 time to fit residues: 2580.0682 Evaluate side-chains 1277 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1231 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 880 TRP Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1123 LYS Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1208 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 793 VAL Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain D residue 1059 ARG Chi-restraints excluded: chain D residue 1096 ASN Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1199 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 501 GLN Chi-restraints excluded: chain E residue 901 GLU Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain E residue 1123 LYS Chi-restraints excluded: chain E residue 1199 THR Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 614 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 0.8980 chunk 272 optimal weight: 7.9990 chunk 407 optimal weight: 0.8980 chunk 205 optimal weight: 0.0050 chunk 134 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 433 optimal weight: 3.9990 chunk 464 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 536 optimal weight: 0.0970 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 677 ASN A 799 GLN A1184 ASN B 404 HIS B 677 ASN B 679 GLN C 363 ASN C 944 ASN D 292 GLN D 404 HIS D 679 GLN D 973 GLN D1184 ASN E 251 GLN E 316 HIS E 320 GLN E 677 ASN E 944 ASN E 973 GLN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 ASN ** F 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1045 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 56498 Z= 0.132 Angle : 0.437 7.574 76597 Z= 0.226 Chirality : 0.042 0.139 8430 Planarity : 0.004 0.035 10121 Dihedral : 3.860 41.672 7752 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.89 % Allowed : 14.53 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.93 (0.10), residues: 7062 helix: 1.61 (0.10), residues: 2598 sheet: 1.08 (0.14), residues: 1416 loop : -0.45 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 466 HIS 0.004 0.001 HIS D 404 PHE 0.022 0.001 PHE D1046 TYR 0.014 0.001 TYR D 761 ARG 0.008 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1257 time to evaluate : 4.619 Fit side-chains REVERT: A 290 GLU cc_start: 0.8626 (pm20) cc_final: 0.8298 (pm20) REVERT: A 1059 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8329 (mtt90) REVERT: A 1208 GLN cc_start: 0.8505 (mt0) cc_final: 0.8262 (mt0) REVERT: B 118 MET cc_start: 0.8846 (mmt) cc_final: 0.8156 (mmt) REVERT: B 290 GLU cc_start: 0.8622 (pm20) cc_final: 0.8371 (pm20) REVERT: B 405 ARG cc_start: 0.8586 (mtm180) cc_final: 0.8291 (mtm180) REVERT: B 902 ASP cc_start: 0.8086 (m-30) cc_final: 0.7847 (m-30) REVERT: B 1059 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8315 (mtt90) REVERT: B 1194 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8392 (ptp90) REVERT: C 152 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8487 (p) REVERT: E 248 ASP cc_start: 0.8556 (m-30) cc_final: 0.8333 (t0) REVERT: E 629 ASP cc_start: 0.8384 (t0) cc_final: 0.8151 (t0) REVERT: E 761 TYR cc_start: 0.8430 (m-80) cc_final: 0.8056 (m-80) REVERT: E 947 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8626 (tt) REVERT: F 257 LEU cc_start: 0.8924 (tp) cc_final: 0.8704 (tp) REVERT: F 405 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8162 (mtm180) REVERT: F 593 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.7585 (tpt) REVERT: F 859 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8433 (ttm170) outliers start: 52 outliers final: 18 residues processed: 1275 average time/residue: 1.6310 time to fit residues: 2544.8712 Evaluate side-chains 1261 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1237 time to evaluate : 4.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 901 GLU Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 593 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 0.0670 chunk 653 optimal weight: 5.9990 chunk 596 optimal weight: 10.0000 chunk 635 optimal weight: 4.9990 chunk 382 optimal weight: 0.5980 chunk 277 optimal weight: 3.9990 chunk 499 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 574 optimal weight: 0.8980 chunk 601 optimal weight: 2.9990 chunk 633 optimal weight: 3.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 799 GLN B 404 HIS B 589 GLN B 677 ASN B 944 ASN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 944 ASN D 404 HIS D 498 ASN D 679 GLN E 251 GLN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1045 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 56498 Z= 0.194 Angle : 0.468 8.298 76597 Z= 0.242 Chirality : 0.043 0.145 8430 Planarity : 0.004 0.039 10121 Dihedral : 3.940 40.076 7752 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.57 % Allowed : 15.19 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.91 (0.10), residues: 7062 helix: 1.57 (0.10), residues: 2598 sheet: 1.09 (0.14), residues: 1416 loop : -0.44 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 466 HIS 0.005 0.001 HIS D 404 PHE 0.025 0.001 PHE F1046 TYR 0.016 0.001 TYR F 761 ARG 0.010 0.000 ARG F 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1244 time to evaluate : 4.733 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8859 (mmt) cc_final: 0.8104 (mmt) REVERT: A 290 GLU cc_start: 0.8633 (pm20) cc_final: 0.8305 (pm20) REVERT: A 1059 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8361 (mtt90) REVERT: A 1208 GLN cc_start: 0.8541 (mt0) cc_final: 0.8292 (mt0) REVERT: B 290 GLU cc_start: 0.8621 (pm20) cc_final: 0.8345 (pm20) REVERT: B 405 ARG cc_start: 0.8590 (mtm180) cc_final: 0.8242 (mtm180) REVERT: B 902 ASP cc_start: 0.8121 (m-30) cc_final: 0.7894 (m-30) REVERT: B 1059 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8382 (mtt90) REVERT: B 1194 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8400 (ptp90) REVERT: C 152 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8468 (p) REVERT: E 248 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8371 (t0) REVERT: E 629 ASP cc_start: 0.8429 (t0) cc_final: 0.8186 (t0) REVERT: E 761 TYR cc_start: 0.8450 (m-80) cc_final: 0.8138 (m-80) REVERT: E 947 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8628 (tt) REVERT: F 257 LEU cc_start: 0.8939 (tp) cc_final: 0.8708 (tp) REVERT: F 405 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8173 (mtm180) REVERT: F 544 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8339 (ttm-80) REVERT: F 593 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.7610 (tpt) REVERT: F 859 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8434 (ttm170) outliers start: 33 outliers final: 21 residues processed: 1255 average time/residue: 1.6664 time to fit residues: 2543.7245 Evaluate side-chains 1258 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1230 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 1096 ASN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 993 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 0.0980 chunk 672 optimal weight: 0.5980 chunk 410 optimal weight: 0.5980 chunk 318 optimal weight: 2.9990 chunk 467 optimal weight: 0.4980 chunk 705 optimal weight: 2.9990 chunk 649 optimal weight: 5.9990 chunk 561 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 799 GLN B 404 HIS B 589 GLN C 944 ASN D 404 HIS D 679 GLN D 973 GLN E 251 GLN E 320 GLN E 944 ASN E 973 GLN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1045 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 56498 Z= 0.183 Angle : 0.465 8.462 76597 Z= 0.241 Chirality : 0.043 0.145 8430 Planarity : 0.004 0.043 10121 Dihedral : 3.922 38.193 7752 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.62 % Allowed : 15.45 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.94 (0.10), residues: 7062 helix: 1.57 (0.10), residues: 2598 sheet: 1.12 (0.14), residues: 1416 loop : -0.42 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 466 HIS 0.005 0.001 HIS D 404 PHE 0.024 0.001 PHE F1046 TYR 0.016 0.001 TYR F 761 ARG 0.010 0.000 ARG F 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14124 Ramachandran restraints generated. 7062 Oldfield, 0 Emsley, 7062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1229 time to evaluate : 4.750 Fit side-chains REVERT: A 118 MET cc_start: 0.8860 (mmt) cc_final: 0.8106 (mmt) REVERT: A 290 GLU cc_start: 0.8632 (pm20) cc_final: 0.8302 (pm20) REVERT: A 1059 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8364 (mtt90) REVERT: A 1208 GLN cc_start: 0.8520 (mt0) cc_final: 0.8269 (mt0) REVERT: B 290 GLU cc_start: 0.8621 (pm20) cc_final: 0.8344 (pm20) REVERT: B 405 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8302 (mtm180) REVERT: B 902 ASP cc_start: 0.8116 (m-30) cc_final: 0.7894 (m-30) REVERT: B 1059 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8335 (mtt90) REVERT: B 1194 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8403 (ptp90) REVERT: C 152 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 800 MET cc_start: 0.8482 (mmt) cc_final: 0.8064 (mmt) REVERT: E 248 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8369 (t0) REVERT: E 629 ASP cc_start: 0.8424 (t0) cc_final: 0.8184 (t0) REVERT: E 761 TYR cc_start: 0.8427 (m-80) cc_final: 0.8110 (m-80) REVERT: E 947 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8633 (tt) REVERT: F 257 LEU cc_start: 0.8937 (tp) cc_final: 0.8709 (tp) REVERT: F 405 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8166 (mtm180) REVERT: F 470 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8214 (mtt90) REVERT: F 544 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: F 593 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.7611 (tpt) REVERT: F 859 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8437 (ttm170) REVERT: I 72 ARG cc_start: 0.8926 (ttt-90) cc_final: 0.8671 (ttt-90) outliers start: 36 outliers final: 23 residues processed: 1241 average time/residue: 1.6932 time to fit residues: 2553.8129 Evaluate side-chains 1261 residues out of total 5892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1230 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 1059 ARG Chi-restraints excluded: chain B residue 1194 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 1096 ASN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 920 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 901 GLU Chi-restraints excluded: chain E residue 947 LEU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain F residue 593 MET Chi-restraints excluded: chain F residue 614 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 446 optimal weight: 0.8980 chunk 598 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 517 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 562 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 577 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN A 799 GLN B 404 HIS C 944 ASN D 404 HIS D 498 ASN D 679 GLN D 973 GLN E 251 GLN E 320 GLN E 944 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 944 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1045 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.104682 restraints weight = 74563.758| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.44 r_work: 0.3411 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 56498 Z= 0.178 Angle : 0.464 9.381 76597 Z= 0.240 Chirality : 0.043 0.144 8430 Planarity : 0.004 0.043 10121 Dihedral : 3.901 36.887 7752 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.75 % Allowed : 15.37 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.95 (0.10), residues: 7062 helix: 1.58 (0.10), residues: 2598 sheet: 1.13 (0.14), residues: 1416 loop : -0.41 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 466 HIS 0.005 0.001 HIS D 404 PHE 0.024 0.001 PHE F1046 TYR 0.016 0.001 TYR F 761 ARG 0.010 0.000 ARG F 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32191.29 seconds wall clock time: 551 minutes 55.52 seconds (33115.52 seconds total)