Starting phenix.real_space_refine on Sat Mar 7 08:45:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pee_20315/03_2026/6pee_20315_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pee_20315/03_2026/6pee_20315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pee_20315/03_2026/6pee_20315_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pee_20315/03_2026/6pee_20315_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pee_20315/03_2026/6pee_20315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pee_20315/03_2026/6pee_20315.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 25620 2.51 5 N 7050 2.21 5 O 7680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 255 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40440 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 9.15, per 1000 atoms: 0.23 Number of scatterers: 40440 At special positions: 0 Unit cell: (160.74, 167.58, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 7680 8.00 N 7050 7.00 C 25620 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 - 3.00 Amino acid : True - 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: 2.95 Conformation dependent library (CDL) restraints added in 1.8 seconds 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9570 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 75 sheets defined 18.4% alpha, 58.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.512A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.973A pdb=" N HIS A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS A 489 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 490 " --> pdb=" O LEU A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 490' Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE A 497 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 549 removed outlier: 3.972A pdb=" N TRP A 549 " --> pdb=" O LEU A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.512A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.974A pdb=" N HIS B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.520A pdb=" N LYS B 489 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 490 " --> pdb=" O LEU B 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 486 through 490' Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.556A pdb=" N PHE B 497 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.582A pdb=" N VAL B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 532 " --> pdb=" O GLU B 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 removed outlier: 3.971A pdb=" N TRP B 549 " --> pdb=" O LEU B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 549' Processing helix chain 'B' and resid 550 through 555 removed outlier: 4.062A pdb=" N LEU B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS C 489 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 490 " --> pdb=" O LEU C 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 486 through 490' Processing helix chain 'C' and resid 493 through 497 removed outlier: 3.556A pdb=" N PHE C 497 " --> pdb=" O GLY C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP C 549 " --> pdb=" O LEU C 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 546 through 549' Processing helix chain 'C' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.512A pdb=" N ALA D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 486 through 490 removed outlier: 3.519A pdb=" N LYS D 489 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 490 " --> pdb=" O LEU D 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 486 through 490' Processing helix chain 'D' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE D 497 " --> pdb=" O GLY D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 532 " --> pdb=" O GLU D 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP D 549 " --> pdb=" O LEU D 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 546 through 549' Processing helix chain 'D' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU D 554 " --> pdb=" O VAL D 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 295 removed outlier: 3.973A pdb=" N HIS F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 293 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS F 489 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 490 " --> pdb=" O LEU F 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 486 through 490' Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.554A pdb=" N PHE F 497 " --> pdb=" O GLY F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 538 removed outlier: 3.582A pdb=" N VAL F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN F 531 " --> pdb=" O SER F 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN F 532 " --> pdb=" O GLU F 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 535 " --> pdb=" O ASN F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP F 549 " --> pdb=" O LEU F 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 546 through 549' Processing helix chain 'F' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU F 554 " --> pdb=" O VAL F 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA G 210 " --> pdb=" O GLY G 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 211 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 295 removed outlier: 3.974A pdb=" N HIS G 288 " --> pdb=" O ALA G 284 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 293 " --> pdb=" O PHE G 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'G' and resid 486 through 490 removed outlier: 3.519A pdb=" N LYS G 489 " --> pdb=" O PHE G 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU G 490 " --> pdb=" O LEU G 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 486 through 490' Processing helix chain 'G' and resid 493 through 497 removed outlier: 3.554A pdb=" N PHE G 497 " --> pdb=" O GLY G 494 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN G 531 " --> pdb=" O SER G 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 532 " --> pdb=" O GLU G 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS G 535 " --> pdb=" O ASN G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP G 549 " --> pdb=" O LEU G 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 546 through 549' Processing helix chain 'G' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU G 554 " --> pdb=" O VAL G 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 removed outlier: 3.512A pdb=" N ALA H 210 " --> pdb=" O GLY H 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 211 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU H 212 " --> pdb=" O ALA H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 3.973A pdb=" N HIS H 288 " --> pdb=" O ALA H 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 293 " --> pdb=" O PHE H 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 444 Processing helix chain 'H' and resid 486 through 490 removed outlier: 3.520A pdb=" N LYS H 489 " --> pdb=" O PHE H 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 490 " --> pdb=" O LEU H 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 486 through 490' Processing helix chain 'H' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE H 497 " --> pdb=" O GLY H 494 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 538 removed outlier: 3.582A pdb=" N VAL H 530 " --> pdb=" O ALA H 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN H 531 " --> pdb=" O SER H 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 532 " --> pdb=" O GLU H 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS H 535 " --> pdb=" O ASN H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 549 removed outlier: 3.972A pdb=" N TRP H 549 " --> pdb=" O LEU H 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 546 through 549' Processing helix chain 'H' and resid 550 through 555 removed outlier: 4.062A pdb=" N LEU H 554 " --> pdb=" O VAL H 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 removed outlier: 3.512A pdb=" N ALA I 210 " --> pdb=" O GLY I 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE I 211 " --> pdb=" O ILE I 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS I 288 " --> pdb=" O ALA I 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU I 293 " --> pdb=" O PHE I 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 296 " --> pdb=" O MET I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 444 Processing helix chain 'I' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS I 489 " --> pdb=" O PHE I 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU I 490 " --> pdb=" O LEU I 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 486 through 490' Processing helix chain 'I' and resid 493 through 497 removed outlier: 3.556A pdb=" N PHE I 497 " --> pdb=" O GLY I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN I 531 " --> pdb=" O SER I 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN I 532 " --> pdb=" O GLU I 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS I 535 " --> pdb=" O ASN I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 549 removed outlier: 3.972A pdb=" N TRP I 549 " --> pdb=" O LEU I 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 546 through 549' Processing helix chain 'I' and resid 550 through 555 removed outlier: 4.060A pdb=" N LEU I 554 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 215 removed outlier: 3.511A pdb=" N ALA J 210 " --> pdb=" O GLY J 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 211 " --> pdb=" O ILE J 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS J 288 " --> pdb=" O ALA J 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU J 293 " --> pdb=" O PHE J 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 444 Processing helix chain 'J' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS J 489 " --> pdb=" O PHE J 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU J 490 " --> pdb=" O LEU J 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 486 through 490' Processing helix chain 'J' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE J 497 " --> pdb=" O GLY J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 525 through 538 removed outlier: 3.582A pdb=" N VAL J 530 " --> pdb=" O ALA J 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN J 531 " --> pdb=" O SER J 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN J 532 " --> pdb=" O GLU J 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS J 535 " --> pdb=" O ASN J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 549 removed outlier: 3.972A pdb=" N TRP J 549 " --> pdb=" O LEU J 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 546 through 549' Processing helix chain 'J' and resid 550 through 555 removed outlier: 4.062A pdb=" N LEU J 554 " --> pdb=" O VAL J 550 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA K 210 " --> pdb=" O GLY K 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 211 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS K 288 " --> pdb=" O ALA K 284 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 293 " --> pdb=" O PHE K 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA K 296 " --> pdb=" O MET K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 444 Processing helix chain 'K' and resid 486 through 490 removed outlier: 3.519A pdb=" N LYS K 489 " --> pdb=" O PHE K 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU K 490 " --> pdb=" O LEU K 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 486 through 490' Processing helix chain 'K' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE K 497 " --> pdb=" O GLY K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL K 530 " --> pdb=" O ALA K 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN K 531 " --> pdb=" O SER K 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS K 535 " --> pdb=" O ASN K 531 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP K 549 " --> pdb=" O LEU K 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 546 through 549' Processing helix chain 'K' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU K 554 " --> pdb=" O VAL K 550 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA L 210 " --> pdb=" O GLY L 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE L 211 " --> pdb=" O ILE L 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 295 removed outlier: 3.974A pdb=" N HIS L 288 " --> pdb=" O ALA L 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 293 " --> pdb=" O PHE L 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 444 Processing helix chain 'L' and resid 486 through 490 removed outlier: 3.519A pdb=" N LYS L 489 " --> pdb=" O PHE L 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU L 490 " --> pdb=" O LEU L 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 486 through 490' Processing helix chain 'L' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE L 497 " --> pdb=" O GLY L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 538 removed outlier: 3.583A pdb=" N VAL L 530 " --> pdb=" O ALA L 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN L 531 " --> pdb=" O SER L 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN L 532 " --> pdb=" O GLU L 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS L 535 " --> pdb=" O ASN L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP L 549 " --> pdb=" O LEU L 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 546 through 549' Processing helix chain 'L' and resid 550 through 555 removed outlier: 4.062A pdb=" N LEU L 554 " --> pdb=" O VAL L 550 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA M 210 " --> pdb=" O GLY M 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE M 211 " --> pdb=" O ILE M 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU M 212 " --> pdb=" O ALA M 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS M 288 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU M 293 " --> pdb=" O PHE M 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS M 295 " --> pdb=" O GLU M 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA M 296 " --> pdb=" O MET M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 440 through 444 Processing helix chain 'M' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS M 489 " --> pdb=" O PHE M 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU M 490 " --> pdb=" O LEU M 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 486 through 490' Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE M 497 " --> pdb=" O GLY M 494 " (cutoff:3.500A) Processing helix chain 'M' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL M 530 " --> pdb=" O ALA M 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN M 531 " --> pdb=" O SER M 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN M 532 " --> pdb=" O GLU M 528 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS M 535 " --> pdb=" O ASN M 531 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP M 549 " --> pdb=" O LEU M 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 546 through 549' Processing helix chain 'M' and resid 550 through 555 removed outlier: 4.060A pdb=" N LEU M 554 " --> pdb=" O VAL M 550 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA N 210 " --> pdb=" O GLY N 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE N 211 " --> pdb=" O ILE N 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU N 212 " --> pdb=" O ALA N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 298 removed outlier: 3.973A pdb=" N HIS N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 295 " --> pdb=" O GLU N 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA N 296 " --> pdb=" O MET N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 440 through 444 Processing helix chain 'N' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS N 489 " --> pdb=" O PHE N 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU N 490 " --> pdb=" O LEU N 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 486 through 490' Processing helix chain 'N' and resid 493 through 497 removed outlier: 3.556A pdb=" N PHE N 497 " --> pdb=" O GLY N 494 " (cutoff:3.500A) Processing helix chain 'N' and resid 525 through 538 removed outlier: 3.581A pdb=" N VAL N 530 " --> pdb=" O ALA N 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN N 531 " --> pdb=" O SER N 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN N 532 " --> pdb=" O GLU N 528 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS N 535 " --> pdb=" O ASN N 531 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 549 removed outlier: 3.972A pdb=" N TRP N 549 " --> pdb=" O LEU N 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 546 through 549' Processing helix chain 'N' and resid 550 through 555 removed outlier: 4.060A pdb=" N LEU N 554 " --> pdb=" O VAL N 550 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 215 removed outlier: 3.513A pdb=" N ALA O 210 " --> pdb=" O GLY O 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE O 211 " --> pdb=" O ILE O 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU O 212 " --> pdb=" O ALA O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 295 removed outlier: 3.974A pdb=" N HIS O 288 " --> pdb=" O ALA O 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 293 " --> pdb=" O PHE O 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS O 295 " --> pdb=" O GLU O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 440 through 444 Processing helix chain 'O' and resid 486 through 490 removed outlier: 3.518A pdb=" N LYS O 489 " --> pdb=" O PHE O 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU O 490 " --> pdb=" O LEU O 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 486 through 490' Processing helix chain 'O' and resid 493 through 497 removed outlier: 3.555A pdb=" N PHE O 497 " --> pdb=" O GLY O 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 525 through 538 removed outlier: 3.583A pdb=" N VAL O 530 " --> pdb=" O ALA O 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN O 531 " --> pdb=" O SER O 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN O 532 " --> pdb=" O GLU O 528 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS O 535 " --> pdb=" O ASN O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 546 through 549 removed outlier: 3.973A pdb=" N TRP O 549 " --> pdb=" O LEU O 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 546 through 549' Processing helix chain 'O' and resid 550 through 555 removed outlier: 4.061A pdb=" N LEU O 554 " --> pdb=" O VAL O 550 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 215 removed outlier: 3.512A pdb=" N ALA P 210 " --> pdb=" O GLY P 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE P 211 " --> pdb=" O ILE P 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU P 212 " --> pdb=" O ALA P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 295 removed outlier: 3.975A pdb=" N HIS P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU P 293 " --> pdb=" O PHE P 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS P 295 " --> pdb=" O GLU P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 440 through 444 Processing helix chain 'P' and resid 486 through 490 removed outlier: 3.519A pdb=" N LYS P 489 " --> pdb=" O PHE P 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU P 490 " --> pdb=" O LEU P 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 486 through 490' Processing helix chain 'P' and resid 493 through 497 removed outlier: 3.554A pdb=" N PHE P 497 " --> pdb=" O GLY P 494 " (cutoff:3.500A) Processing helix chain 'P' and resid 525 through 538 removed outlier: 3.582A pdb=" N VAL P 530 " --> pdb=" O ALA P 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN P 531 " --> pdb=" O SER P 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN P 532 " --> pdb=" O GLU P 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS P 535 " --> pdb=" O ASN P 531 " (cutoff:3.500A) Processing helix chain 'P' and resid 546 through 549 removed outlier: 3.972A pdb=" N TRP P 549 " --> pdb=" O LEU P 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 546 through 549' Processing helix chain 'P' and resid 550 through 555 removed outlier: 4.060A pdb=" N LEU P 554 " --> pdb=" O VAL P 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 184 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.308A pdb=" N PHE A 352 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER B 338 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 354 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 363 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 365 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS A 303 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 319 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 511 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 470 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 513 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 468 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 15.933A pdb=" N LEU A 467 " --> pdb=" O GLN P 376 " (cutoff:3.500A) removed outlier: 12.860A pdb=" N GLN P 376 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 469 " --> pdb=" O LEU P 374 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN P 364 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.801A pdb=" N LYS P 363 " --> pdb=" O SER P 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA P 365 " --> pdb=" O ASN P 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS P 303 " --> pdb=" O ILE P 518 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU P 319 " --> pdb=" O LYS P 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE P 511 " --> pdb=" O GLY P 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY P 470 " --> pdb=" O PHE P 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE P 513 " --> pdb=" O LEU P 468 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU P 468 " --> pdb=" O ILE P 513 " (cutoff:3.500A) removed outlier: 15.916A pdb=" N LEU P 467 " --> pdb=" O GLN O 376 " (cutoff:3.500A) removed outlier: 12.836A pdb=" N GLN O 376 " --> pdb=" O LEU P 467 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL P 469 " --> pdb=" O LEU O 374 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE O 352 " --> pdb=" O GLY P 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER P 338 " --> pdb=" O PHE O 352 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA O 354 " --> pdb=" O SER P 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 327 through 328 removed outlier: 6.317A pdb=" N PHE O 352 " --> pdb=" O GLY P 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER P 338 " --> pdb=" O PHE O 352 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA O 354 " --> pdb=" O SER P 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS O 363 " --> pdb=" O SER O 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA O 365 " --> pdb=" O ASN O 314 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS O 303 " --> pdb=" O ILE O 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU O 319 " --> pdb=" O LYS O 502 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE O 511 " --> pdb=" O GLY O 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY O 470 " --> pdb=" O PHE O 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE O 513 " --> pdb=" O LEU O 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU O 468 " --> pdb=" O ILE O 513 " (cutoff:3.500A) removed outlier: 15.919A pdb=" N LEU O 467 " --> pdb=" O GLN N 376 " (cutoff:3.500A) removed outlier: 12.837A pdb=" N GLN N 376 " --> pdb=" O LEU O 467 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL O 469 " --> pdb=" O LEU N 374 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE N 352 " --> pdb=" O GLY O 336 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER O 338 " --> pdb=" O PHE N 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA N 354 " --> pdb=" O SER O 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 327 through 328 removed outlier: 6.319A pdb=" N PHE N 352 " --> pdb=" O GLY O 336 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER O 338 " --> pdb=" O PHE N 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA N 354 " --> pdb=" O SER O 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS N 363 " --> pdb=" O SER N 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA N 365 " --> pdb=" O ASN N 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS N 303 " --> pdb=" O ILE N 518 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU N 319 " --> pdb=" O LYS N 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE N 511 " --> pdb=" O GLY N 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY N 470 " --> pdb=" O PHE N 511 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE N 513 " --> pdb=" O LEU N 468 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU N 468 " --> pdb=" O ILE N 513 " (cutoff:3.500A) removed outlier: 15.919A pdb=" N LEU N 467 " --> pdb=" O GLN M 376 " (cutoff:3.500A) removed outlier: 12.839A pdb=" N GLN M 376 " --> pdb=" O LEU N 467 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL N 469 " --> pdb=" O LEU M 374 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE M 352 " --> pdb=" O GLY N 336 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER N 338 " --> pdb=" O PHE M 352 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA M 354 " --> pdb=" O SER N 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 327 through 328 removed outlier: 6.309A pdb=" N PHE M 352 " --> pdb=" O GLY N 336 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER N 338 " --> pdb=" O PHE M 352 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA M 354 " --> pdb=" O SER N 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS M 363 " --> pdb=" O SER M 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA M 365 " --> pdb=" O ASN M 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS M 303 " --> pdb=" O ILE M 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU M 319 " --> pdb=" O LYS M 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE M 511 " --> pdb=" O GLY M 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY M 470 " --> pdb=" O PHE M 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE M 513 " --> pdb=" O LEU M 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU M 468 " --> pdb=" O ILE M 513 " (cutoff:3.500A) removed outlier: 15.918A pdb=" N LEU M 467 " --> pdb=" O GLN L 376 " (cutoff:3.500A) removed outlier: 12.835A pdb=" N GLN L 376 " --> pdb=" O LEU M 467 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL M 469 " --> pdb=" O LEU L 374 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE L 352 " --> pdb=" O GLY M 336 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N SER M 338 " --> pdb=" O PHE L 352 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA L 354 " --> pdb=" O SER M 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 327 through 328 removed outlier: 6.316A pdb=" N PHE L 352 " --> pdb=" O GLY M 336 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N SER M 338 " --> pdb=" O PHE L 352 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA L 354 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS L 363 " --> pdb=" O SER L 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 365 " --> pdb=" O ASN L 314 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS L 303 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU L 319 " --> pdb=" O LYS L 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE L 511 " --> pdb=" O GLY L 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 470 " --> pdb=" O PHE L 511 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE L 513 " --> pdb=" O LEU L 468 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU L 468 " --> pdb=" O ILE L 513 " (cutoff:3.500A) removed outlier: 15.949A pdb=" N LEU L 467 " --> pdb=" O GLN K 376 " (cutoff:3.500A) removed outlier: 12.869A pdb=" N GLN K 376 " --> pdb=" O LEU L 467 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL L 469 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN K 364 " --> pdb=" O ASP L 479 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE K 352 " --> pdb=" O GLY L 336 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER L 338 " --> pdb=" O PHE K 352 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA K 354 " --> pdb=" O SER L 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 327 through 328 removed outlier: 6.241A pdb=" N PHE K 352 " --> pdb=" O GLY L 336 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER L 338 " --> pdb=" O PHE K 352 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA K 354 " --> pdb=" O SER L 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS K 363 " --> pdb=" O SER K 316 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA K 365 " --> pdb=" O ASN K 314 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS K 303 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU K 319 " --> pdb=" O LYS K 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE K 511 " --> pdb=" O GLY K 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY K 470 " --> pdb=" O PHE K 511 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE K 513 " --> pdb=" O LEU K 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU K 468 " --> pdb=" O ILE K 513 " (cutoff:3.500A) removed outlier: 15.890A pdb=" N LEU K 467 " --> pdb=" O GLN J 376 " (cutoff:3.500A) removed outlier: 12.832A pdb=" N GLN J 376 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL K 469 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN J 364 " --> pdb=" O ASP K 479 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU J 360 " --> pdb=" O SER K 483 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE J 352 " --> pdb=" O GLY K 336 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER K 338 " --> pdb=" O PHE J 352 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA J 354 " --> pdb=" O SER K 338 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 327 through 328 removed outlier: 6.545A pdb=" N PHE J 352 " --> pdb=" O GLY K 336 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER K 338 " --> pdb=" O PHE J 352 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA J 354 " --> pdb=" O SER K 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS J 363 " --> pdb=" O SER J 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA J 365 " --> pdb=" O ASN J 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS J 303 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU J 319 " --> pdb=" O LYS J 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE J 511 " --> pdb=" O GLY J 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY J 470 " --> pdb=" O PHE J 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE J 513 " --> pdb=" O LEU J 468 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU J 468 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 15.865A pdb=" N LEU J 467 " --> pdb=" O GLN I 376 " (cutoff:3.500A) removed outlier: 12.754A pdb=" N GLN I 376 " --> pdb=" O LEU J 467 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL J 469 " --> pdb=" O LEU I 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 327 through 328 removed outlier: 3.801A pdb=" N LYS I 363 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA I 365 " --> pdb=" O ASN I 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS I 303 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU I 319 " --> pdb=" O LYS I 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE I 511 " --> pdb=" O GLY I 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY I 470 " --> pdb=" O PHE I 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE I 513 " --> pdb=" O LEU I 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU I 468 " --> pdb=" O ILE I 513 " (cutoff:3.500A) removed outlier: 16.064A pdb=" N LEU I 467 " --> pdb=" O GLN H 376 " (cutoff:3.500A) removed outlier: 12.960A pdb=" N GLN H 376 " --> pdb=" O LEU I 467 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL I 469 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN H 364 " --> pdb=" O ASP I 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 327 through 328 removed outlier: 3.801A pdb=" N LYS H 363 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA H 365 " --> pdb=" O ASN H 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS H 303 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU H 319 " --> pdb=" O LYS H 502 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE H 511 " --> pdb=" O GLY H 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY H 470 " --> pdb=" O PHE H 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE H 513 " --> pdb=" O LEU H 468 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU H 468 " --> pdb=" O ILE H 513 " (cutoff:3.500A) removed outlier: 15.919A pdb=" N LEU H 467 " --> pdb=" O GLN G 376 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N GLN G 376 " --> pdb=" O LEU H 467 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL H 469 " --> pdb=" O LEU G 374 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE G 352 " --> pdb=" O GLY H 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER H 338 " --> pdb=" O PHE G 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA G 354 " --> pdb=" O SER H 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 327 through 328 removed outlier: 6.317A pdb=" N PHE G 352 " --> pdb=" O GLY H 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER H 338 " --> pdb=" O PHE G 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA G 354 " --> pdb=" O SER H 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 363 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA G 365 " --> pdb=" O ASN G 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS G 303 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU G 319 " --> pdb=" O LYS G 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE G 511 " --> pdb=" O GLY G 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G 470 " --> pdb=" O PHE G 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE G 513 " --> pdb=" O LEU G 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU G 468 " --> pdb=" O ILE G 513 " (cutoff:3.500A) removed outlier: 15.918A pdb=" N LEU G 467 " --> pdb=" O GLN F 376 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N GLN F 376 " --> pdb=" O LEU G 467 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL G 469 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE F 352 " --> pdb=" O GLY G 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER G 338 " --> pdb=" O PHE F 352 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA F 354 " --> pdb=" O SER G 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 327 through 328 removed outlier: 6.318A pdb=" N PHE F 352 " --> pdb=" O GLY G 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER G 338 " --> pdb=" O PHE F 352 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA F 354 " --> pdb=" O SER G 338 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS F 363 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 365 " --> pdb=" O ASN F 314 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS F 303 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 319 " --> pdb=" O LYS F 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE F 511 " --> pdb=" O GLY F 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 470 " --> pdb=" O PHE F 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE F 513 " --> pdb=" O LEU F 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU F 468 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 15.918A pdb=" N LEU F 467 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N GLN D 376 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL F 469 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE D 352 " --> pdb=" O GLY F 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER F 338 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA D 354 " --> pdb=" O SER F 338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 327 through 328 removed outlier: 6.318A pdb=" N PHE D 352 " --> pdb=" O GLY F 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER F 338 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA D 354 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 363 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 365 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS D 303 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU D 319 " --> pdb=" O LYS D 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 511 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 470 " --> pdb=" O PHE D 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE D 513 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU D 468 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 15.918A pdb=" N LEU D 467 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 12.839A pdb=" N GLN C 376 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 469 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE C 352 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER D 338 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA C 354 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 327 through 328 removed outlier: 6.319A pdb=" N PHE C 352 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER D 338 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA C 354 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 363 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 365 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS C 303 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 319 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 511 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 470 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 513 " --> pdb=" O LEU C 468 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU C 468 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 15.919A pdb=" N LEU C 467 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N GLN B 376 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 469 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 352 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER C 338 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 354 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 328 removed outlier: 6.320A pdb=" N PHE B 352 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER C 338 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 354 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 363 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 365 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS B 303 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B 319 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 511 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 470 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 513 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 468 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 15.925A pdb=" N LEU B 467 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 12.835A pdb=" N GLN A 376 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 469 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 352 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER B 338 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 354 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA P 400 " --> pdb=" O LEU P 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU P 393 " --> pdb=" O ALA P 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU P 402 " --> pdb=" O THR P 391 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.641A pdb=" N THR A 457 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 415 through 416 removed outlier: 4.579A pdb=" N ALA A 400 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 393 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 402 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 386 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 452 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR B 457 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA B 400 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 393 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 402 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR C 457 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA C 400 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 393 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU C 402 " --> pdb=" O THR C 391 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR D 457 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 415 through 416 removed outlier: 4.579A pdb=" N ALA D 400 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 393 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 402 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR F 457 " --> pdb=" O LEU F 426 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA F 400 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F 393 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 402 " --> pdb=" O THR F 391 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR G 457 " --> pdb=" O LEU G 426 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA G 400 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU G 393 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU G 402 " --> pdb=" O THR G 391 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR H 457 " --> pdb=" O LEU H 426 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA H 400 " --> pdb=" O LEU H 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H 393 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU H 402 " --> pdb=" O THR H 391 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR I 457 " --> pdb=" O LEU I 426 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 415 through 416 removed outlier: 4.579A pdb=" N ALA I 400 " --> pdb=" O LEU I 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU I 393 " --> pdb=" O ALA I 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU I 402 " --> pdb=" O THR I 391 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR J 457 " --> pdb=" O LEU J 426 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 415 through 416 removed outlier: 4.581A pdb=" N ALA J 400 " --> pdb=" O LEU J 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU J 393 " --> pdb=" O ALA J 400 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU J 402 " --> pdb=" O THR J 391 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 386 " --> pdb=" O ARG K 452 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG K 452 " --> pdb=" O ASN J 386 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 450 " --> pdb=" O THR J 388 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR K 457 " --> pdb=" O LEU K 426 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 415 through 416 removed outlier: 4.581A pdb=" N ALA K 400 " --> pdb=" O LEU K 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU K 393 " --> pdb=" O ALA K 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU K 402 " --> pdb=" O THR K 391 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR L 457 " --> pdb=" O LEU L 426 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA L 400 " --> pdb=" O LEU L 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU L 393 " --> pdb=" O ALA L 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 402 " --> pdb=" O THR L 391 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 432 through 433 removed outlier: 3.642A pdb=" N THR M 457 " --> pdb=" O LEU M 426 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA M 400 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU M 393 " --> pdb=" O ALA M 400 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU M 402 " --> pdb=" O THR M 391 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR N 457 " --> pdb=" O LEU N 426 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA N 400 " --> pdb=" O LEU N 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU N 393 " --> pdb=" O ALA N 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU N 402 " --> pdb=" O THR N 391 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR O 457 " --> pdb=" O LEU O 426 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 415 through 416 removed outlier: 4.580A pdb=" N ALA O 400 " --> pdb=" O LEU O 393 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU O 393 " --> pdb=" O ALA O 400 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU O 402 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 432 through 433 removed outlier: 3.643A pdb=" N THR P 457 " --> pdb=" O LEU P 426 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 179 through 184 Processing sheet with id=AF4, first strand: chain 'B' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 179 through 184 Processing sheet with id=AF6, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN C 200 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 179 through 184 Processing sheet with id=AF8, first strand: chain 'D' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN D 200 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 179 through 184 Processing sheet with id=AG1, first strand: chain 'F' and resid 193 through 197 removed outlier: 3.671A pdb=" N GLN F 200 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 179 through 184 Processing sheet with id=AG3, first strand: chain 'G' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN G 200 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 179 through 184 Processing sheet with id=AG5, first strand: chain 'H' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN H 200 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 179 through 184 Processing sheet with id=AG7, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.671A pdb=" N GLN I 200 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 179 through 184 Processing sheet with id=AG9, first strand: chain 'J' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN J 200 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 179 through 184 Processing sheet with id=AH2, first strand: chain 'K' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN K 200 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 179 through 184 Processing sheet with id=AH4, first strand: chain 'L' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN L 200 " --> pdb=" O LEU L 197 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 179 through 184 Processing sheet with id=AH6, first strand: chain 'M' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN M 200 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 179 through 184 Processing sheet with id=AH8, first strand: chain 'N' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN N 200 " --> pdb=" O LEU N 197 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 179 through 184 Processing sheet with id=AI1, first strand: chain 'O' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN O 200 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 179 through 184 Processing sheet with id=AI3, first strand: chain 'P' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN P 200 " --> pdb=" O LEU P 197 " (cutoff:3.500A) 2158 hydrogen bonds defined for protein. 5712 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: 10.73 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13307 1.34 - 1.46: 4919 1.46 - 1.57: 22589 1.57 - 1.69: 0 1.69 - 1.80: 180 Bond restraints: 40995 Sorted by residual: bond pdb=" N1 LDA D1001 " pdb=" O1 LDA D1001 " ideal model delta sigma weight residual 1.354 1.248 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N1 LDA C1001 " pdb=" O1 LDA C1001 " ideal model delta sigma weight residual 1.354 1.248 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" N1 LDA I1001 " pdb=" O1 LDA I1001 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N1 LDA G1002 " pdb=" O1 LDA G1002 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N1 LDA O1001 " pdb=" O1 LDA O1001 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 40990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 52647 1.66 - 3.33: 2362 3.33 - 4.99: 221 4.99 - 6.65: 165 6.65 - 8.32: 75 Bond angle restraints: 55470 Sorted by residual: angle pdb=" C GLY O 332 " pdb=" N ASP O 333 " pdb=" CA ASP O 333 " ideal model delta sigma weight residual 122.08 128.54 -6.46 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C GLY L 332 " pdb=" N ASP L 333 " pdb=" CA ASP L 333 " ideal model delta sigma weight residual 122.08 128.53 -6.45 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C GLY B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" C GLY K 332 " pdb=" N ASP K 333 " pdb=" CA ASP K 333 " ideal model delta sigma weight residual 122.08 128.49 -6.41 1.47e+00 4.63e-01 1.90e+01 angle pdb=" C GLY C 332 " pdb=" N ASP C 333 " pdb=" CA ASP C 333 " ideal model delta sigma weight residual 122.08 128.48 -6.40 1.47e+00 4.63e-01 1.90e+01 ... (remaining 55465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 22519 16.98 - 33.96: 1961 33.96 - 50.94: 390 50.94 - 67.93: 120 67.93 - 84.91: 45 Dihedral angle restraints: 25035 sinusoidal: 10215 harmonic: 14820 Sorted by residual: dihedral pdb=" CA GLY K 217 " pdb=" C GLY K 217 " pdb=" N GLU K 218 " pdb=" CA GLU K 218 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY M 217 " pdb=" C GLY M 217 " pdb=" N GLU M 218 " pdb=" CA GLU M 218 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY I 217 " pdb=" C GLY I 217 " pdb=" N GLU I 218 " pdb=" CA GLU I 218 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 25032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4406 0.044 - 0.088: 1353 0.088 - 0.132: 530 0.132 - 0.177: 176 0.177 - 0.221: 60 Chirality restraints: 6525 Sorted by residual: chirality pdb=" CA ASP D 333 " pdb=" N ASP D 333 " pdb=" C ASP D 333 " pdb=" CB ASP D 333 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASP I 333 " pdb=" N ASP I 333 " pdb=" C ASP I 333 " pdb=" CB ASP I 333 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASP M 333 " pdb=" N ASP M 333 " pdb=" C ASP M 333 " pdb=" CB ASP M 333 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 6522 not shown) Planarity restraints: 7035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG N 370 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO N 371 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO N 371 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 371 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 370 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO L 371 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO L 371 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 371 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P 370 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO P 371 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO P 371 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO P 371 " -0.037 5.00e-02 4.00e+02 ... (remaining 7032 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2252 2.73 - 3.27: 32835 3.27 - 3.81: 58326 3.81 - 4.36: 69528 4.36 - 4.90: 131615 Nonbonded interactions: 294556 Sorted by model distance: nonbonded pdb=" O SER I 537 " pdb=" ND2 ASN K 477 " model vdw 2.186 3.120 nonbonded pdb=" O LYS I 301 " pdb=" NH2 ARG J 460 " model vdw 2.276 3.120 nonbonded pdb=" O SER H 537 " pdb=" ND2 ASN J 477 " model vdw 2.305 3.120 nonbonded pdb=" OG1 THR N 323 " pdb=" O LEU N 496 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR K 323 " pdb=" O LEU K 496 " model vdw 2.343 3.040 ... (remaining 294551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'B' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'C' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'D' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'F' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'G' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'H' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'I' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'J' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'K' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'L' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'M' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'N' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'O' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'P' and (resid 175 through 601 or (resid 602 through 603 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or nam \ e C9 or name CM1 or name CM2 or name N1 or name O1 )))) } 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.760 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.007 0.106 40995 Z= 0.305 Angle : 0.867 8.315 55470 Z= 0.467 Chirality : 0.055 0.221 6525 Planarity : 0.006 0.068 7035 Dihedral : 13.951 84.906 15465 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.34 % Allowed : 8.20 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.10), residues: 5115 helix: -5.10 (0.04), residues: 855 sheet: -1.53 (0.09), residues: 2700 loop : -2.67 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 474 TYR 0.008 0.001 TYR N 406 PHE 0.012 0.002 PHE B 511 TRP 0.007 0.001 TRP D 309 HIS 0.001 0.000 HIS G 463 Details of bonding type rmsd covalent geometry : bond 0.00665 (40995) covalent geometry : angle 0.86660 (55470) hydrogen bonds : bond 0.30764 ( 2056) hydrogen bonds : angle 9.70964 ( 5712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 455 time to evaluate : 1.559 Fit side-chains REVERT: A 183 MET cc_start: 0.8597 (mtt) cc_final: 0.8341 (mtt) REVERT: A 200 GLN cc_start: 0.7573 (pt0) cc_final: 0.7211 (pt0) REVERT: A 289 PHE cc_start: 0.8271 (t80) cc_final: 0.8043 (t80) REVERT: A 292 MET cc_start: 0.8253 (mmp) cc_final: 0.8048 (mmm) REVERT: A 361 GLU cc_start: 0.7450 (tt0) cc_final: 0.7207 (tt0) REVERT: A 512 MET cc_start: 0.8778 (mtm) cc_final: 0.8211 (mtt) REVERT: A 536 GLN cc_start: 0.8493 (mt0) cc_final: 0.8176 (mt0) REVERT: B 183 MET cc_start: 0.8619 (mtt) cc_final: 0.8229 (mpp) REVERT: B 289 PHE cc_start: 0.8512 (t80) cc_final: 0.7782 (t80) REVERT: B 298 ASP cc_start: 0.7935 (t0) cc_final: 0.7554 (t0) REVERT: B 320 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7217 (mtt90) REVERT: B 424 MET cc_start: 0.8706 (mtm) cc_final: 0.8225 (mtm) REVERT: B 496 LEU cc_start: 0.8873 (mp) cc_final: 0.8662 (mt) REVERT: C 328 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8216 (p) REVERT: D 331 ILE cc_start: 0.8044 (mm) cc_final: 0.7772 (tt) REVERT: F 200 GLN cc_start: 0.8366 (pt0) cc_final: 0.8120 (pt0) REVERT: F 202 MET cc_start: 0.8384 (mmm) cc_final: 0.8044 (mmm) REVERT: F 512 MET cc_start: 0.8356 (mtm) cc_final: 0.7956 (mtm) REVERT: G 183 MET cc_start: 0.8862 (mtt) cc_final: 0.8299 (mtm) REVERT: G 289 PHE cc_start: 0.8081 (t80) cc_final: 0.7787 (t80) REVERT: G 424 MET cc_start: 0.8240 (mtm) cc_final: 0.7840 (mtm) REVERT: I 328 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8239 (p) REVERT: I 475 ASP cc_start: 0.8297 (m-30) cc_final: 0.8024 (m-30) REVERT: I 512 MET cc_start: 0.8443 (mtm) cc_final: 0.8001 (mtt) REVERT: J 199 ASP cc_start: 0.7962 (p0) cc_final: 0.7761 (p0) REVERT: J 292 MET cc_start: 0.8271 (mmp) cc_final: 0.8065 (mmp) REVERT: J 424 MET cc_start: 0.8888 (mtm) cc_final: 0.8305 (mtp) REVERT: J 486 PHE cc_start: 0.7573 (t80) cc_final: 0.7367 (t80) REVERT: K 272 TYR cc_start: 0.8890 (t80) cc_final: 0.8469 (t80) REVERT: K 429 GLU cc_start: 0.7704 (tt0) cc_final: 0.7387 (tt0) REVERT: L 200 GLN cc_start: 0.8315 (pt0) cc_final: 0.8056 (pt0) REVERT: L 292 MET cc_start: 0.8304 (mmp) cc_final: 0.7963 (mmm) REVERT: L 328 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8160 (p) REVERT: L 512 MET cc_start: 0.8451 (mtm) cc_final: 0.7569 (mtp) REVERT: L 540 TRP cc_start: 0.8377 (t60) cc_final: 0.7986 (t60) REVERT: M 402 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6904 (mm-30) REVERT: M 409 MET cc_start: 0.7672 (ttt) cc_final: 0.6983 (ttm) REVERT: M 424 MET cc_start: 0.8681 (mtm) cc_final: 0.8394 (mtp) REVERT: N 216 GLN cc_start: 0.7931 (tt0) cc_final: 0.7718 (tt0) REVERT: N 328 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7779 (p) REVERT: N 360 GLU cc_start: 0.7576 (tt0) cc_final: 0.7252 (tt0) REVERT: O 183 MET cc_start: 0.8413 (mtt) cc_final: 0.8163 (mtm) REVERT: O 200 GLN cc_start: 0.7870 (pt0) cc_final: 0.7343 (pt0) REVERT: O 272 TYR cc_start: 0.8727 (t80) cc_final: 0.8320 (t80) REVERT: O 274 ASP cc_start: 0.8662 (t0) cc_final: 0.7936 (t0) REVERT: O 292 MET cc_start: 0.8456 (mmp) cc_final: 0.8138 (mmm) REVERT: P 202 MET cc_start: 0.8246 (mmm) cc_final: 0.7770 (mmt) REVERT: P 274 ASP cc_start: 0.8446 (t0) cc_final: 0.8217 (t0) REVERT: P 389 PHE cc_start: 0.7430 (t80) cc_final: 0.7079 (t80) REVERT: P 424 MET cc_start: 0.8530 (mtm) cc_final: 0.8295 (mtm) REVERT: P 486 PHE cc_start: 0.7426 (t80) cc_final: 0.7113 (t80) REVERT: P 512 MET cc_start: 0.8384 (mtm) cc_final: 0.8171 (mtp) outliers start: 15 outliers final: 4 residues processed: 470 average time/residue: 0.2694 time to fit residues: 202.0599 Evaluate side-chains 329 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 321 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain I residue 328 SER Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain M residue 328 SER Chi-restraints excluded: chain N residue 328 SER Chi-restraints excluded: chain O residue 328 SER Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 432 ASN B 432 ASN C 421 GLN C 432 ASN D 421 GLN D 432 ASN F 341 GLN F 432 ASN G 432 ASN H 432 ASN I 421 GLN I 432 ASN J 432 ASN K 432 ASN L 432 ASN M 432 ASN N 341 GLN N 432 ASN O 432 ASN P 432 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.082108 restraints weight = 56753.701| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.09 r_work: 0.2764 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 40995 Z= 0.205 Angle : 0.635 6.443 55470 Z= 0.341 Chirality : 0.046 0.168 6525 Planarity : 0.006 0.076 7035 Dihedral : 7.493 59.576 5933 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.24 % Allowed : 10.87 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.11), residues: 5115 helix: -3.55 (0.12), residues: 705 sheet: -0.55 (0.10), residues: 2610 loop : -2.31 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 370 TYR 0.017 0.002 TYR M 195 PHE 0.021 0.002 PHE D 389 TRP 0.014 0.001 TRP O 309 HIS 0.005 0.001 HIS P 303 Details of bonding type rmsd covalent geometry : bond 0.00486 (40995) covalent geometry : angle 0.63497 (55470) hydrogen bonds : bond 0.05720 ( 2056) hydrogen bonds : angle 5.65466 ( 5712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 366 time to evaluate : 1.520 Fit side-chains REVERT: A 183 MET cc_start: 0.8974 (mtt) cc_final: 0.8580 (mtt) REVERT: A 289 PHE cc_start: 0.8702 (t80) cc_final: 0.8301 (t80) REVERT: A 361 GLU cc_start: 0.8366 (tt0) cc_final: 0.7934 (tt0) REVERT: A 363 LYS cc_start: 0.8890 (tttt) cc_final: 0.8471 (tttm) REVERT: A 389 PHE cc_start: 0.8282 (t80) cc_final: 0.8055 (t80) REVERT: A 409 MET cc_start: 0.8825 (ttp) cc_final: 0.8576 (ttm) REVERT: B 177 ARG cc_start: 0.6719 (mmm-85) cc_final: 0.6161 (mmm-85) REVERT: B 212 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 285 GLU cc_start: 0.7841 (tp30) cc_final: 0.7620 (tm-30) REVERT: B 298 ASP cc_start: 0.7888 (t0) cc_final: 0.7442 (t0) REVERT: B 424 MET cc_start: 0.9189 (mtm) cc_final: 0.8661 (mtm) REVERT: B 427 ASP cc_start: 0.8278 (m-30) cc_final: 0.8015 (t0) REVERT: B 482 GLN cc_start: 0.8441 (mt0) cc_final: 0.8134 (mt0) REVERT: B 496 LEU cc_start: 0.9482 (mp) cc_final: 0.9117 (mt) REVERT: B 536 GLN cc_start: 0.8698 (mt0) cc_final: 0.8382 (tt0) REVERT: C 212 GLU cc_start: 0.7966 (tt0) cc_final: 0.7311 (tm-30) REVERT: C 402 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7440 (mm-30) REVERT: D 361 GLU cc_start: 0.7979 (tt0) cc_final: 0.7084 (tm-30) REVERT: D 363 LYS cc_start: 0.8725 (tttt) cc_final: 0.8404 (ttmm) REVERT: D 411 ARG cc_start: 0.8586 (ttp-170) cc_final: 0.8377 (ttp80) REVERT: D 432 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7729 (p0) REVERT: F 202 MET cc_start: 0.8609 (mmm) cc_final: 0.8051 (mmm) REVERT: F 512 MET cc_start: 0.8748 (mtm) cc_final: 0.8344 (mtm) REVERT: G 183 MET cc_start: 0.9038 (mtt) cc_final: 0.8598 (mtm) REVERT: G 202 MET cc_start: 0.8294 (mmm) cc_final: 0.8071 (mtp) REVERT: G 212 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7967 (tt0) REVERT: G 289 PHE cc_start: 0.8192 (t80) cc_final: 0.7948 (t80) REVERT: G 363 LYS cc_start: 0.9063 (tttt) cc_final: 0.8742 (ttmm) REVERT: G 424 MET cc_start: 0.9167 (mtm) cc_final: 0.8859 (mtm) REVERT: H 212 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7518 (tm-30) REVERT: H 402 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7718 (mm-30) REVERT: H 432 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7242 (p0) REVERT: I 212 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8132 (tm-30) REVERT: I 361 GLU cc_start: 0.8649 (tt0) cc_final: 0.8181 (tt0) REVERT: I 382 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8761 (tt) REVERT: I 389 PHE cc_start: 0.8356 (t80) cc_final: 0.7936 (t80) REVERT: I 424 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8234 (ptp) REVERT: I 432 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7513 (p0) REVERT: I 475 ASP cc_start: 0.8700 (m-30) cc_final: 0.8293 (m-30) REVERT: I 512 MET cc_start: 0.8946 (mtm) cc_final: 0.8351 (mtt) REVERT: I 550 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9077 (p) REVERT: J 272 TYR cc_start: 0.8482 (t80) cc_final: 0.8240 (t80) REVERT: J 337 VAL cc_start: 0.7923 (t) cc_final: 0.7719 (t) REVERT: J 486 PHE cc_start: 0.8119 (t80) cc_final: 0.7769 (t80) REVERT: K 200 GLN cc_start: 0.7742 (pt0) cc_final: 0.7298 (pt0) REVERT: K 212 GLU cc_start: 0.8480 (tt0) cc_final: 0.8256 (tt0) REVERT: K 429 GLU cc_start: 0.8566 (tt0) cc_final: 0.8198 (tt0) REVERT: K 482 GLN cc_start: 0.8405 (mt0) cc_final: 0.8138 (mt0) REVERT: L 177 ARG cc_start: 0.6669 (mmm-85) cc_final: 0.6132 (mmm-85) REVERT: L 274 ASP cc_start: 0.8235 (t0) cc_final: 0.7598 (t0) REVERT: L 512 MET cc_start: 0.8781 (mtm) cc_final: 0.8096 (mtp) REVERT: L 540 TRP cc_start: 0.8425 (t60) cc_final: 0.8140 (t60) REVERT: M 177 ARG cc_start: 0.6717 (mtp85) cc_final: 0.6259 (ttp80) REVERT: M 183 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (mtt) REVERT: M 409 MET cc_start: 0.8197 (ttt) cc_final: 0.7514 (ttm) REVERT: M 424 MET cc_start: 0.8826 (mtm) cc_final: 0.8612 (mtm) REVERT: N 212 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7793 (tm-30) REVERT: N 312 ASP cc_start: 0.8344 (t70) cc_final: 0.7896 (t0) REVERT: N 341 GLN cc_start: 0.7961 (mt0) cc_final: 0.7682 (mt0) REVERT: N 360 GLU cc_start: 0.8043 (tt0) cc_final: 0.7394 (tt0) REVERT: N 363 LYS cc_start: 0.8855 (tttt) cc_final: 0.8545 (tttm) REVERT: N 410 ILE cc_start: 0.8780 (mt) cc_final: 0.8453 (mm) REVERT: N 432 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7098 (p0) REVERT: O 200 GLN cc_start: 0.7527 (pt0) cc_final: 0.6927 (pt0) REVERT: O 274 ASP cc_start: 0.8897 (t0) cc_final: 0.8110 (t0) REVERT: O 363 LYS cc_start: 0.8837 (tttt) cc_final: 0.8376 (mtpt) REVERT: O 402 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8654 (mm-30) REVERT: O 432 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7363 (p0) REVERT: O 482 GLN cc_start: 0.8328 (mt0) cc_final: 0.7980 (mt0) REVERT: P 197 LEU cc_start: 0.8647 (mp) cc_final: 0.8433 (mp) REVERT: P 202 MET cc_start: 0.8571 (mmm) cc_final: 0.8291 (mmt) REVERT: P 274 ASP cc_start: 0.9027 (t0) cc_final: 0.8630 (t0) REVERT: P 319 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7697 (tm-30) REVERT: P 360 GLU cc_start: 0.8364 (tt0) cc_final: 0.8132 (tt0) REVERT: P 409 MET cc_start: 0.8558 (ttm) cc_final: 0.8032 (ttp) REVERT: P 427 ASP cc_start: 0.8275 (m-30) cc_final: 0.7977 (m-30) REVERT: P 486 PHE cc_start: 0.7881 (t80) cc_final: 0.7596 (t80) REVERT: P 512 MET cc_start: 0.8640 (mtm) cc_final: 0.8281 (mtp) outliers start: 55 outliers final: 28 residues processed: 405 average time/residue: 0.2538 time to fit residues: 166.6333 Evaluate side-chains 350 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain H residue 432 ASN Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 432 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 432 ASN Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 432 ASN Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 493 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 200 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 385 optimal weight: 0.8980 chunk 13 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 470 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 432 ASN A 506 ASN B 341 GLN B 432 ASN C 200 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN D 432 ASN D 506 ASN F 398 ASN G 421 GLN H 398 ASN H 432 ASN H 506 ASN I 432 ASN J 421 GLN J 432 ASN K 398 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 536 GLN L 432 ASN M 303 HIS M 432 ASN M 506 ASN N 432 ASN N 506 ASN O 266 ASN O 398 ASN P 432 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.082956 restraints weight = 56589.157| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.02 r_work: 0.2760 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 40995 Z= 0.230 Angle : 0.633 10.295 55470 Z= 0.338 Chirality : 0.046 0.170 6525 Planarity : 0.005 0.081 7035 Dihedral : 6.849 59.949 5925 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.92 % Allowed : 12.93 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.11), residues: 5115 helix: -2.60 (0.16), residues: 675 sheet: -0.01 (0.10), residues: 2565 loop : -2.33 (0.12), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 198 TYR 0.023 0.002 TYR M 195 PHE 0.027 0.002 PHE O 511 TRP 0.014 0.001 TRP O 309 HIS 0.004 0.001 HIS P 303 Details of bonding type rmsd covalent geometry : bond 0.00558 (40995) covalent geometry : angle 0.63344 (55470) hydrogen bonds : bond 0.05486 ( 2056) hydrogen bonds : angle 5.35096 ( 5712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 332 time to evaluate : 1.597 Fit side-chains REVERT: A 177 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6745 (mmm-85) REVERT: A 183 MET cc_start: 0.8971 (mtt) cc_final: 0.8681 (mtt) REVERT: A 200 GLN cc_start: 0.7779 (pt0) cc_final: 0.7394 (pt0) REVERT: A 361 GLU cc_start: 0.8166 (tt0) cc_final: 0.7810 (tt0) REVERT: A 363 LYS cc_start: 0.8875 (tttt) cc_final: 0.8663 (ttmm) REVERT: A 389 PHE cc_start: 0.8196 (t80) cc_final: 0.7970 (t80) REVERT: A 409 MET cc_start: 0.8743 (ttp) cc_final: 0.8493 (ttm) REVERT: B 177 ARG cc_start: 0.6991 (mmm-85) cc_final: 0.6665 (mmm-85) REVERT: B 212 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 427 ASP cc_start: 0.8281 (m-30) cc_final: 0.7987 (t0) REVERT: B 523 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9116 (p) REVERT: B 536 GLN cc_start: 0.8875 (mt0) cc_final: 0.8613 (tt0) REVERT: C 212 GLU cc_start: 0.7987 (tt0) cc_final: 0.7346 (tm-30) REVERT: C 312 ASP cc_start: 0.8270 (t0) cc_final: 0.8054 (t70) REVERT: C 361 GLU cc_start: 0.7895 (tt0) cc_final: 0.7469 (tm-30) REVERT: C 402 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7367 (mm-30) REVERT: D 363 LYS cc_start: 0.8702 (tttt) cc_final: 0.8501 (mtpt) REVERT: D 406 TYR cc_start: 0.8761 (p90) cc_final: 0.8184 (p90) REVERT: D 411 ARG cc_start: 0.8611 (ttp-170) cc_final: 0.8387 (ttp80) REVERT: D 427 ASP cc_start: 0.8351 (m-30) cc_final: 0.8040 (m-30) REVERT: D 432 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7670 (p0) REVERT: F 202 MET cc_start: 0.8563 (mmm) cc_final: 0.7893 (mtt) REVERT: F 512 MET cc_start: 0.8779 (mtm) cc_final: 0.8431 (mtm) REVERT: F 523 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 177 ARG cc_start: 0.7040 (mmm-85) cc_final: 0.6386 (mmm-85) REVERT: G 183 MET cc_start: 0.9093 (mtt) cc_final: 0.8658 (mtm) REVERT: G 202 MET cc_start: 0.8233 (mmm) cc_final: 0.8019 (mtp) REVERT: G 289 PHE cc_start: 0.8345 (t80) cc_final: 0.8137 (t80) REVERT: G 363 LYS cc_start: 0.8931 (tttt) cc_final: 0.8707 (ttmm) REVERT: G 424 MET cc_start: 0.9208 (mtm) cc_final: 0.8850 (mtm) REVERT: H 183 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8297 (ptp) REVERT: H 212 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7597 (tm-30) REVERT: H 402 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8048 (mm-30) REVERT: H 427 ASP cc_start: 0.8486 (m-30) cc_final: 0.8005 (m-30) REVERT: H 429 GLU cc_start: 0.8297 (tt0) cc_final: 0.8076 (tt0) REVERT: I 212 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8285 (tm-30) REVERT: I 361 GLU cc_start: 0.8617 (tt0) cc_final: 0.8264 (tt0) REVERT: I 382 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8802 (tt) REVERT: I 389 PHE cc_start: 0.8393 (t80) cc_final: 0.8117 (t80) REVERT: I 424 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8244 (ptp) REVERT: I 432 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8207 (p0) REVERT: I 475 ASP cc_start: 0.8708 (m-30) cc_final: 0.8335 (m-30) REVERT: I 496 LEU cc_start: 0.8951 (mp) cc_final: 0.8631 (tp) REVERT: I 512 MET cc_start: 0.8966 (mtm) cc_final: 0.8513 (mtt) REVERT: I 550 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9053 (p) REVERT: J 183 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8351 (ptp) REVERT: J 200 GLN cc_start: 0.8399 (pt0) cc_final: 0.7778 (pt0) REVERT: J 274 ASP cc_start: 0.8608 (t0) cc_final: 0.8222 (t0) REVERT: J 432 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7552 (p0) REVERT: K 200 GLN cc_start: 0.7850 (pt0) cc_final: 0.7385 (pt0) REVERT: K 212 GLU cc_start: 0.8482 (tt0) cc_final: 0.8262 (tt0) REVERT: K 319 GLU cc_start: 0.7914 (tt0) cc_final: 0.7556 (tm-30) REVERT: K 429 GLU cc_start: 0.8548 (tt0) cc_final: 0.8161 (tt0) REVERT: K 482 GLN cc_start: 0.8472 (mt0) cc_final: 0.8139 (mt0) REVERT: K 536 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: L 177 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.5949 (ttt-90) REVERT: L 363 LYS cc_start: 0.8908 (tttt) cc_final: 0.8327 (mtpp) REVERT: L 512 MET cc_start: 0.8939 (mtm) cc_final: 0.8387 (mtp) REVERT: L 540 TRP cc_start: 0.8422 (t60) cc_final: 0.8131 (t60) REVERT: M 177 ARG cc_start: 0.6712 (mtp85) cc_final: 0.5905 (mtp85) REVERT: M 285 GLU cc_start: 0.7754 (tp30) cc_final: 0.7387 (tm-30) REVERT: N 212 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7832 (tm-30) REVERT: N 312 ASP cc_start: 0.8368 (t70) cc_final: 0.7891 (t0) REVERT: N 360 GLU cc_start: 0.7969 (tt0) cc_final: 0.7372 (tt0) REVERT: N 363 LYS cc_start: 0.8844 (tttt) cc_final: 0.8511 (ttmt) REVERT: N 410 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8435 (mm) REVERT: N 432 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8441 (p0) REVERT: O 200 GLN cc_start: 0.7537 (pt0) cc_final: 0.6925 (pt0) REVERT: O 274 ASP cc_start: 0.8875 (t0) cc_final: 0.8183 (t0) REVERT: O 363 LYS cc_start: 0.8902 (tttt) cc_final: 0.8469 (mtpt) REVERT: O 482 GLN cc_start: 0.8432 (mt0) cc_final: 0.7868 (mt0) REVERT: O 486 PHE cc_start: 0.8486 (t80) cc_final: 0.8282 (t80) REVERT: O 536 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: O 540 TRP cc_start: 0.8106 (t60) cc_final: 0.7423 (t-100) REVERT: P 212 GLU cc_start: 0.8219 (tt0) cc_final: 0.7760 (tm-30) REVERT: P 319 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7865 (tm-30) REVERT: P 360 GLU cc_start: 0.8315 (tt0) cc_final: 0.8099 (tt0) REVERT: P 409 MET cc_start: 0.8467 (ttm) cc_final: 0.7975 (ttp) REVERT: P 427 ASP cc_start: 0.8208 (m-30) cc_final: 0.7956 (m-30) REVERT: P 486 PHE cc_start: 0.7810 (t80) cc_final: 0.7590 (t80) REVERT: P 512 MET cc_start: 0.8583 (mtm) cc_final: 0.8357 (mtt) outliers start: 129 outliers final: 87 residues processed: 434 average time/residue: 0.2377 time to fit residues: 173.0285 Evaluate side-chains 405 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 304 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 432 ASN Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 536 GLN Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 432 ASN Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 432 ASN Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 510 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 291 GLU Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 432 ASN Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 536 GLN Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 184 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 375 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 426 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 HIS B 376 GLN C 421 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN D 303 HIS D 432 ASN G 506 ASN I 341 GLN I 432 ASN J 432 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 536 GLN N 432 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.081599 restraints weight = 56978.548| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.07 r_work: 0.2744 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 40995 Z= 0.288 Angle : 0.672 7.237 55470 Z= 0.358 Chirality : 0.048 0.167 6525 Planarity : 0.006 0.087 7035 Dihedral : 6.764 59.886 5925 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.93 % Allowed : 14.21 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.11), residues: 5115 helix: -2.20 (0.17), residues: 675 sheet: 0.08 (0.10), residues: 2565 loop : -2.34 (0.12), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 198 TYR 0.018 0.002 TYR M 195 PHE 0.031 0.002 PHE O 511 TRP 0.014 0.002 TRP H 309 HIS 0.005 0.001 HIS O 303 Details of bonding type rmsd covalent geometry : bond 0.00707 (40995) covalent geometry : angle 0.67172 (55470) hydrogen bonds : bond 0.05569 ( 2056) hydrogen bonds : angle 5.45523 ( 5712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 311 time to evaluate : 1.573 Fit side-chains REVERT: A 183 MET cc_start: 0.8994 (mtt) cc_final: 0.8723 (mtt) REVERT: A 200 GLN cc_start: 0.7909 (pt0) cc_final: 0.7490 (pt0) REVERT: A 361 GLU cc_start: 0.8106 (tt0) cc_final: 0.7786 (tt0) REVERT: A 363 LYS cc_start: 0.8869 (tttt) cc_final: 0.8618 (ttmm) REVERT: A 389 PHE cc_start: 0.8348 (t80) cc_final: 0.8067 (t80) REVERT: A 409 MET cc_start: 0.8749 (ttp) cc_final: 0.8501 (ttm) REVERT: B 212 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 341 GLN cc_start: 0.7483 (mt0) cc_final: 0.7061 (mt0) REVERT: B 427 ASP cc_start: 0.8276 (m-30) cc_final: 0.8001 (t0) REVERT: B 523 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9130 (p) REVERT: B 536 GLN cc_start: 0.8825 (mt0) cc_final: 0.8532 (tt0) REVERT: C 177 ARG cc_start: 0.6563 (mmm-85) cc_final: 0.6125 (mmm-85) REVERT: C 212 GLU cc_start: 0.7992 (tt0) cc_final: 0.7336 (tm-30) REVERT: C 312 ASP cc_start: 0.8496 (t0) cc_final: 0.8183 (t70) REVERT: C 361 GLU cc_start: 0.7959 (tt0) cc_final: 0.7504 (tm-30) REVERT: C 402 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 361 GLU cc_start: 0.8068 (tt0) cc_final: 0.7119 (tm-30) REVERT: D 363 LYS cc_start: 0.8699 (tttt) cc_final: 0.8411 (ttmm) REVERT: D 406 TYR cc_start: 0.8831 (p90) cc_final: 0.8257 (p90) REVERT: D 411 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.8353 (ttp80) REVERT: D 427 ASP cc_start: 0.8384 (m-30) cc_final: 0.8048 (m-30) REVERT: F 202 MET cc_start: 0.8560 (mmm) cc_final: 0.7910 (mtt) REVERT: F 512 MET cc_start: 0.8761 (mtm) cc_final: 0.8483 (mtm) REVERT: F 523 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8788 (p) REVERT: G 177 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6416 (mmm-85) REVERT: G 183 MET cc_start: 0.9116 (mtt) cc_final: 0.8701 (mtm) REVERT: G 202 MET cc_start: 0.8368 (mmm) cc_final: 0.7777 (mmm) REVERT: G 212 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8031 (tt0) REVERT: G 289 PHE cc_start: 0.8398 (t80) cc_final: 0.8160 (t80) REVERT: G 363 LYS cc_start: 0.8916 (tttt) cc_final: 0.8622 (ttmm) REVERT: G 424 MET cc_start: 0.9247 (mtm) cc_final: 0.8878 (mtm) REVERT: G 502 LYS cc_start: 0.8215 (mttt) cc_final: 0.7853 (mtmm) REVERT: H 183 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8325 (ptp) REVERT: H 212 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7514 (tm-30) REVERT: H 402 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8182 (mm-30) REVERT: H 427 ASP cc_start: 0.8501 (m-30) cc_final: 0.7994 (m-30) REVERT: H 429 GLU cc_start: 0.8373 (tt0) cc_final: 0.8153 (tt0) REVERT: H 447 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7955 (tt) REVERT: I 212 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8348 (tm-30) REVERT: I 293 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (tp) REVERT: I 382 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8806 (tt) REVERT: I 389 PHE cc_start: 0.8388 (t80) cc_final: 0.8144 (t80) REVERT: I 424 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8332 (ptp) REVERT: I 447 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7954 (tp) REVERT: I 475 ASP cc_start: 0.8685 (m-30) cc_final: 0.8454 (m-30) REVERT: I 496 LEU cc_start: 0.8946 (mp) cc_final: 0.8586 (tp) REVERT: I 512 MET cc_start: 0.8999 (mtm) cc_final: 0.8620 (mtt) REVERT: I 550 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9033 (p) REVERT: J 183 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8368 (ptp) REVERT: J 200 GLN cc_start: 0.8421 (pt0) cc_final: 0.7801 (pt0) REVERT: J 274 ASP cc_start: 0.8607 (t0) cc_final: 0.8080 (t0) REVERT: J 364 GLN cc_start: 0.8312 (tt0) cc_final: 0.8080 (tt0) REVERT: J 432 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7706 (p0) REVERT: K 212 GLU cc_start: 0.8518 (tt0) cc_final: 0.8289 (tt0) REVERT: K 319 GLU cc_start: 0.7847 (tt0) cc_final: 0.7610 (tm-30) REVERT: K 429 GLU cc_start: 0.8581 (tt0) cc_final: 0.8226 (tt0) REVERT: K 482 GLN cc_start: 0.8429 (mt0) cc_final: 0.8105 (mt0) REVERT: L 177 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6071 (ttt-90) REVERT: L 363 LYS cc_start: 0.8926 (tttt) cc_final: 0.8309 (mtpp) REVERT: L 512 MET cc_start: 0.9060 (mtm) cc_final: 0.8819 (mtm) REVERT: L 540 TRP cc_start: 0.8416 (t60) cc_final: 0.8127 (t60) REVERT: M 177 ARG cc_start: 0.6906 (mtp85) cc_final: 0.6030 (mtp85) REVERT: M 200 GLN cc_start: 0.8113 (pt0) cc_final: 0.7782 (pt0) REVERT: M 285 GLU cc_start: 0.7853 (tp30) cc_final: 0.7453 (tm-30) REVERT: N 212 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7822 (tm-30) REVERT: N 360 GLU cc_start: 0.7936 (tt0) cc_final: 0.7387 (tt0) REVERT: N 363 LYS cc_start: 0.8865 (tttt) cc_final: 0.8542 (ttmt) REVERT: N 410 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8474 (mm) REVERT: N 432 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8392 (p0) REVERT: N 523 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8759 (p) REVERT: O 200 GLN cc_start: 0.7664 (pt0) cc_final: 0.6971 (pt0) REVERT: O 212 GLU cc_start: 0.8671 (tt0) cc_final: 0.8111 (tm-30) REVERT: O 274 ASP cc_start: 0.8834 (t0) cc_final: 0.8150 (t0) REVERT: O 384 ASP cc_start: 0.9001 (t70) cc_final: 0.8774 (t0) REVERT: O 482 GLN cc_start: 0.8567 (mt0) cc_final: 0.8035 (mt0) REVERT: O 486 PHE cc_start: 0.8412 (t80) cc_final: 0.8177 (t80) REVERT: O 536 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: O 540 TRP cc_start: 0.8138 (t60) cc_final: 0.7466 (t-100) REVERT: P 319 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7623 (tm-30) REVERT: P 360 GLU cc_start: 0.8302 (tt0) cc_final: 0.8083 (tt0) REVERT: P 427 ASP cc_start: 0.8169 (m-30) cc_final: 0.7850 (m-30) REVERT: P 512 MET cc_start: 0.8659 (mtm) cc_final: 0.8445 (mtt) outliers start: 174 outliers final: 138 residues processed: 456 average time/residue: 0.2307 time to fit residues: 178.8860 Evaluate side-chains 456 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 303 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 432 ASN Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 291 GLU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 432 ASN Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain O residue 536 GLN Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 478 THR Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 533 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 5 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 357 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 443 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 437 optimal weight: 0.9990 chunk 302 optimal weight: 0.9980 chunk 488 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 398 ASN A 432 ASN B 421 GLN B 432 ASN C 398 ASN D 398 ASN L 398 ASN L 421 GLN L 432 ASN M 432 ASN M 482 GLN N 398 ASN N 421 GLN N 432 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084787 restraints weight = 56175.848| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.08 r_work: 0.2799 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40995 Z= 0.123 Angle : 0.530 7.811 55470 Z= 0.284 Chirality : 0.045 0.154 6525 Planarity : 0.005 0.076 7035 Dihedral : 5.955 59.333 5925 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.48 % Allowed : 15.44 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.11), residues: 5115 helix: -1.69 (0.18), residues: 705 sheet: 0.15 (0.10), residues: 2670 loop : -2.29 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 397 TYR 0.011 0.001 TYR F 195 PHE 0.020 0.001 PHE M 289 TRP 0.010 0.001 TRP H 309 HIS 0.002 0.000 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00290 (40995) covalent geometry : angle 0.52989 (55470) hydrogen bonds : bond 0.03999 ( 2056) hydrogen bonds : angle 4.87330 ( 5712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 349 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8874 (mtt) cc_final: 0.8637 (mtt) REVERT: A 200 GLN cc_start: 0.7743 (pt0) cc_final: 0.7336 (pt0) REVERT: A 361 GLU cc_start: 0.8079 (tt0) cc_final: 0.7731 (tt0) REVERT: A 363 LYS cc_start: 0.8808 (tttt) cc_final: 0.8530 (ttmm) REVERT: A 389 PHE cc_start: 0.8150 (t80) cc_final: 0.7865 (t80) REVERT: A 409 MET cc_start: 0.8652 (ttp) cc_final: 0.8414 (ttm) REVERT: A 555 ASP cc_start: 0.7640 (m-30) cc_final: 0.7189 (t0) REVERT: B 427 ASP cc_start: 0.8302 (m-30) cc_final: 0.7978 (t0) REVERT: B 523 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9119 (p) REVERT: B 536 GLN cc_start: 0.8758 (mt0) cc_final: 0.8419 (tt0) REVERT: C 177 ARG cc_start: 0.6612 (mmm-85) cc_final: 0.6206 (mmm-85) REVERT: C 212 GLU cc_start: 0.7829 (tt0) cc_final: 0.7268 (tm-30) REVERT: C 360 GLU cc_start: 0.8119 (tt0) cc_final: 0.7783 (tt0) REVERT: C 361 GLU cc_start: 0.7930 (tt0) cc_final: 0.7383 (tm-30) REVERT: C 363 LYS cc_start: 0.8711 (tttt) cc_final: 0.8276 (ttmm) REVERT: C 399 VAL cc_start: 0.4775 (OUTLIER) cc_final: 0.4430 (m) REVERT: C 402 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7346 (mm-30) REVERT: C 447 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8078 (tt) REVERT: D 363 LYS cc_start: 0.8629 (tttt) cc_final: 0.8381 (mtpp) REVERT: D 406 TYR cc_start: 0.8793 (p90) cc_final: 0.8248 (p90) REVERT: D 447 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7580 (tt) REVERT: F 202 MET cc_start: 0.8521 (mmm) cc_final: 0.7833 (mtt) REVERT: F 387 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7678 (mmm-85) REVERT: F 510 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8631 (m) REVERT: F 512 MET cc_start: 0.8699 (mtm) cc_final: 0.8344 (mtm) REVERT: F 523 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8712 (p) REVERT: G 177 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6783 (mmm-85) REVERT: G 183 MET cc_start: 0.9144 (mtt) cc_final: 0.8545 (mtm) REVERT: G 202 MET cc_start: 0.8172 (mmm) cc_final: 0.7933 (mtp) REVERT: G 341 GLN cc_start: 0.8143 (mt0) cc_final: 0.7917 (mt0) REVERT: G 363 LYS cc_start: 0.8952 (tttt) cc_final: 0.8647 (ttmm) REVERT: G 424 MET cc_start: 0.9197 (mtm) cc_final: 0.8771 (mtm) REVERT: G 502 LYS cc_start: 0.8106 (mttt) cc_final: 0.7802 (mtmm) REVERT: H 177 ARG cc_start: 0.7469 (ttp80) cc_final: 0.6818 (ttm-80) REVERT: H 201 LYS cc_start: 0.9098 (mttm) cc_final: 0.8788 (mtpp) REVERT: H 212 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7388 (tm-30) REVERT: H 427 ASP cc_start: 0.8505 (m-30) cc_final: 0.8072 (m-30) REVERT: H 447 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7858 (tt) REVERT: I 212 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8239 (tm-30) REVERT: I 382 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8754 (tt) REVERT: I 389 PHE cc_start: 0.8304 (t80) cc_final: 0.7986 (t80) REVERT: I 447 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7935 (tp) REVERT: I 496 LEU cc_start: 0.9113 (mp) cc_final: 0.8731 (tp) REVERT: I 512 MET cc_start: 0.8910 (mtm) cc_final: 0.8505 (mtt) REVERT: J 200 GLN cc_start: 0.8331 (pt0) cc_final: 0.7627 (pt0) REVERT: J 304 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9024 (p) REVERT: K 212 GLU cc_start: 0.8637 (tt0) cc_final: 0.8369 (tt0) REVERT: K 429 GLU cc_start: 0.8577 (tt0) cc_final: 0.8262 (tt0) REVERT: K 469 VAL cc_start: 0.9306 (t) cc_final: 0.8964 (p) REVERT: K 482 GLN cc_start: 0.8457 (mt0) cc_final: 0.8159 (mt0) REVERT: L 177 ARG cc_start: 0.6958 (mmm-85) cc_final: 0.6059 (ttt-90) REVERT: L 363 LYS cc_start: 0.8931 (tttt) cc_final: 0.8313 (mtpp) REVERT: L 399 VAL cc_start: 0.3635 (OUTLIER) cc_final: 0.2907 (m) REVERT: L 447 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7792 (tt) REVERT: L 473 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8736 (m) REVERT: L 512 MET cc_start: 0.8989 (mtm) cc_final: 0.8344 (mtp) REVERT: L 540 TRP cc_start: 0.8388 (t60) cc_final: 0.8096 (t60) REVERT: L 556 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6182 (tpp-160) REVERT: M 177 ARG cc_start: 0.6973 (mtp85) cc_final: 0.6474 (ttp80) REVERT: M 285 GLU cc_start: 0.7802 (tp30) cc_final: 0.7520 (tm-30) REVERT: M 447 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (tp) REVERT: M 473 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8869 (m) REVERT: N 212 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7739 (tm-30) REVERT: N 289 PHE cc_start: 0.8068 (t80) cc_final: 0.7698 (t80) REVERT: N 360 GLU cc_start: 0.7900 (tt0) cc_final: 0.7401 (tt0) REVERT: N 363 LYS cc_start: 0.8856 (tttt) cc_final: 0.8566 (ttmt) REVERT: N 410 ILE cc_start: 0.8774 (mt) cc_final: 0.8525 (mm) REVERT: N 432 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8175 (p0) REVERT: N 523 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8774 (p) REVERT: O 200 GLN cc_start: 0.7384 (pt0) cc_final: 0.6653 (pt0) REVERT: O 274 ASP cc_start: 0.8901 (t0) cc_final: 0.8224 (t0) REVERT: O 482 GLN cc_start: 0.8354 (mt0) cc_final: 0.7694 (mt0) REVERT: O 486 PHE cc_start: 0.8425 (t80) cc_final: 0.8162 (t80) REVERT: O 536 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: O 540 TRP cc_start: 0.8148 (t60) cc_final: 0.7556 (t-100) REVERT: P 319 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7899 (tm-30) REVERT: P 360 GLU cc_start: 0.8151 (tt0) cc_final: 0.7924 (tt0) REVERT: P 409 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7982 (ttp) REVERT: P 410 ILE cc_start: 0.9010 (mt) cc_final: 0.8546 (tt) REVERT: P 427 ASP cc_start: 0.7944 (m-30) cc_final: 0.7557 (m-30) REVERT: P 486 PHE cc_start: 0.7670 (t80) cc_final: 0.7417 (t80) REVERT: P 510 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8515 (m) REVERT: P 540 TRP cc_start: 0.8878 (t60) cc_final: 0.8527 (t60) outliers start: 154 outliers final: 87 residues processed: 479 average time/residue: 0.2450 time to fit residues: 194.0940 Evaluate side-chains 427 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 320 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 397 ARG Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 397 ARG Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 432 ASN Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 432 ASN Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain O residue 536 GLN Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 366 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 409 MET Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 533 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 106 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 387 optimal weight: 40.0000 chunk 123 optimal weight: 4.9990 chunk 431 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 496 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 438 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 432 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN I 398 ASN J 432 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 536 GLN ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 432 ASN O 266 ASN O 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.082375 restraints weight = 56909.466| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.10 r_work: 0.2773 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 40995 Z= 0.192 Angle : 0.588 8.215 55470 Z= 0.313 Chirality : 0.046 0.156 6525 Planarity : 0.005 0.082 7035 Dihedral : 5.995 59.122 5925 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.34 % Allowed : 15.10 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.11), residues: 5115 helix: -1.38 (0.20), residues: 675 sheet: 0.20 (0.10), residues: 2670 loop : -2.25 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 397 TYR 0.017 0.001 TYR M 195 PHE 0.030 0.002 PHE F 289 TRP 0.010 0.001 TRP O 309 HIS 0.003 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00470 (40995) covalent geometry : angle 0.58783 (55470) hydrogen bonds : bond 0.04622 ( 2056) hydrogen bonds : angle 5.04685 ( 5712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 315 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8987 (mtt) cc_final: 0.8737 (mtt) REVERT: A 200 GLN cc_start: 0.7821 (pt0) cc_final: 0.7403 (pt0) REVERT: A 341 GLN cc_start: 0.7405 (mt0) cc_final: 0.6928 (mt0) REVERT: A 361 GLU cc_start: 0.8092 (tt0) cc_final: 0.7720 (tt0) REVERT: A 389 PHE cc_start: 0.8182 (t80) cc_final: 0.7876 (t80) REVERT: A 409 MET cc_start: 0.8711 (ttp) cc_final: 0.8497 (ttm) REVERT: A 555 ASP cc_start: 0.7596 (m-30) cc_final: 0.7253 (t0) REVERT: B 427 ASP cc_start: 0.8252 (m-30) cc_final: 0.7966 (t0) REVERT: B 447 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7708 (tt) REVERT: B 523 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9142 (p) REVERT: B 536 GLN cc_start: 0.8789 (mt0) cc_final: 0.8452 (tt0) REVERT: C 177 ARG cc_start: 0.6580 (mmm-85) cc_final: 0.6197 (mmm-85) REVERT: C 212 GLU cc_start: 0.7891 (tt0) cc_final: 0.7317 (tm-30) REVERT: C 361 GLU cc_start: 0.7941 (tt0) cc_final: 0.7394 (tm-30) REVERT: C 363 LYS cc_start: 0.8708 (tttt) cc_final: 0.8310 (ttmm) REVERT: C 389 PHE cc_start: 0.8339 (t80) cc_final: 0.7787 (t80) REVERT: C 399 VAL cc_start: 0.5484 (OUTLIER) cc_final: 0.4983 (m) REVERT: C 402 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7405 (mm-30) REVERT: D 361 GLU cc_start: 0.8061 (tt0) cc_final: 0.7084 (tm-30) REVERT: D 406 TYR cc_start: 0.8838 (p90) cc_final: 0.8265 (p90) REVERT: D 432 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7710 (p0) REVERT: D 447 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7493 (tt) REVERT: F 202 MET cc_start: 0.8528 (mmm) cc_final: 0.7907 (mtt) REVERT: F 387 ARG cc_start: 0.8063 (mmm160) cc_final: 0.7767 (mmm-85) REVERT: F 473 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8579 (m) REVERT: F 512 MET cc_start: 0.8756 (mtm) cc_final: 0.8407 (mtm) REVERT: F 523 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8670 (p) REVERT: G 177 ARG cc_start: 0.7226 (mmm-85) cc_final: 0.6823 (mmm-85) REVERT: G 183 MET cc_start: 0.9125 (mtt) cc_final: 0.8584 (mtm) REVERT: G 202 MET cc_start: 0.8270 (mmm) cc_final: 0.7601 (mmm) REVERT: G 212 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8019 (tt0) REVERT: G 341 GLN cc_start: 0.8154 (mt0) cc_final: 0.7922 (mt0) REVERT: G 363 LYS cc_start: 0.9001 (tttt) cc_final: 0.8783 (ttmm) REVERT: G 424 MET cc_start: 0.9228 (mtm) cc_final: 0.8806 (mtm) REVERT: G 502 LYS cc_start: 0.8151 (mttt) cc_final: 0.7845 (mtmm) REVERT: H 177 ARG cc_start: 0.7440 (ttp80) cc_final: 0.6794 (ttm-80) REVERT: H 183 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8338 (ptp) REVERT: H 201 LYS cc_start: 0.9116 (mttm) cc_final: 0.8834 (mtpp) REVERT: H 212 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7223 (tm-30) REVERT: H 427 ASP cc_start: 0.8505 (m-30) cc_final: 0.8081 (m-30) REVERT: H 447 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7870 (tt) REVERT: I 212 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8295 (tm-30) REVERT: I 293 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7890 (tp) REVERT: I 382 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8783 (tt) REVERT: I 389 PHE cc_start: 0.8419 (t80) cc_final: 0.8140 (t80) REVERT: I 447 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7935 (tp) REVERT: I 496 LEU cc_start: 0.9133 (mp) cc_final: 0.8754 (tp) REVERT: I 512 MET cc_start: 0.8894 (mtm) cc_final: 0.8531 (mtt) REVERT: I 550 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8942 (p) REVERT: J 200 GLN cc_start: 0.8327 (pt0) cc_final: 0.7683 (pt0) REVERT: J 304 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9022 (p) REVERT: J 432 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7586 (p0) REVERT: K 212 GLU cc_start: 0.8542 (tt0) cc_final: 0.8294 (tt0) REVERT: K 289 PHE cc_start: 0.7784 (t80) cc_final: 0.7572 (t80) REVERT: K 429 GLU cc_start: 0.8562 (tt0) cc_final: 0.8256 (tt0) REVERT: K 482 GLN cc_start: 0.8532 (mt0) cc_final: 0.8182 (mt0) REVERT: K 536 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8648 (mt0) REVERT: L 177 ARG cc_start: 0.6961 (mmm-85) cc_final: 0.6113 (ttt-90) REVERT: L 363 LYS cc_start: 0.8956 (tttt) cc_final: 0.8385 (mtpp) REVERT: L 447 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7850 (tt) REVERT: L 512 MET cc_start: 0.8975 (mtm) cc_final: 0.8762 (mtm) REVERT: L 540 TRP cc_start: 0.8408 (t60) cc_final: 0.8126 (t60) REVERT: L 556 ARG cc_start: 0.6795 (ttm170) cc_final: 0.6381 (tpp-160) REVERT: M 177 ARG cc_start: 0.6971 (mtp85) cc_final: 0.6057 (mtp85) REVERT: M 285 GLU cc_start: 0.7860 (tp30) cc_final: 0.7380 (tm-30) REVERT: M 447 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7409 (tp) REVERT: M 473 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8887 (m) REVERT: N 212 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7751 (tm-30) REVERT: N 289 PHE cc_start: 0.8082 (t80) cc_final: 0.7684 (t80) REVERT: N 360 GLU cc_start: 0.7970 (tt0) cc_final: 0.7440 (tt0) REVERT: N 363 LYS cc_start: 0.8880 (tttt) cc_final: 0.8609 (ttmt) REVERT: N 410 ILE cc_start: 0.8799 (mt) cc_final: 0.8477 (mm) REVERT: N 432 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8316 (p0) REVERT: N 523 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8779 (p) REVERT: O 200 GLN cc_start: 0.7592 (pt0) cc_final: 0.6752 (pt0) REVERT: O 274 ASP cc_start: 0.8880 (t0) cc_final: 0.8202 (t0) REVERT: O 482 GLN cc_start: 0.8525 (mt0) cc_final: 0.7879 (mt0) REVERT: O 486 PHE cc_start: 0.8431 (t80) cc_final: 0.8172 (t80) REVERT: O 536 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: O 540 TRP cc_start: 0.8151 (t60) cc_final: 0.7510 (t-100) REVERT: P 319 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7947 (tm-30) REVERT: P 341 GLN cc_start: 0.8167 (mt0) cc_final: 0.7957 (mt0) REVERT: P 360 GLU cc_start: 0.8171 (tt0) cc_final: 0.7912 (tt0) REVERT: P 409 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7865 (ttp) REVERT: P 410 ILE cc_start: 0.9045 (mt) cc_final: 0.8564 (tt) REVERT: P 427 ASP cc_start: 0.8135 (m-30) cc_final: 0.7744 (m-30) REVERT: P 540 TRP cc_start: 0.8914 (t60) cc_final: 0.8519 (t60) outliers start: 192 outliers final: 140 residues processed: 476 average time/residue: 0.2338 time to fit residues: 186.5436 Evaluate side-chains 464 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 301 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 397 ARG Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain K residue 536 GLN Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 397 ARG Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 432 ASN Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 432 ASN Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 427 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain O residue 536 GLN Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 366 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 409 MET Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 478 THR Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 533 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 309 optimal weight: 0.0980 chunk 228 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 265 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 426 optimal weight: 0.8980 chunk 115 optimal weight: 30.0000 chunk 147 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 536 GLN ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 432 ASN ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.084539 restraints weight = 56392.276| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.08 r_work: 0.2796 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40995 Z= 0.140 Angle : 0.552 10.430 55470 Z= 0.294 Chirality : 0.045 0.153 6525 Planarity : 0.005 0.078 7035 Dihedral : 5.736 59.983 5925 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.07 % Allowed : 15.53 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.11), residues: 5115 helix: -1.31 (0.20), residues: 705 sheet: 0.32 (0.10), residues: 2670 loop : -2.24 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 397 TYR 0.011 0.001 TYR P 195 PHE 0.023 0.002 PHE M 289 TRP 0.009 0.001 TRP F 309 HIS 0.002 0.001 HIS P 303 Details of bonding type rmsd covalent geometry : bond 0.00336 (40995) covalent geometry : angle 0.55212 (55470) hydrogen bonds : bond 0.04059 ( 2056) hydrogen bonds : angle 4.84350 ( 5712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 331 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.7767 (pt0) cc_final: 0.7361 (pt0) REVERT: A 361 GLU cc_start: 0.8090 (tt0) cc_final: 0.7712 (tt0) REVERT: A 389 PHE cc_start: 0.8138 (t80) cc_final: 0.7894 (t80) REVERT: A 409 MET cc_start: 0.8651 (ttp) cc_final: 0.8429 (ttm) REVERT: A 555 ASP cc_start: 0.7615 (m-30) cc_final: 0.7131 (t0) REVERT: B 427 ASP cc_start: 0.8263 (m-30) cc_final: 0.7962 (t0) REVERT: B 523 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9141 (p) REVERT: B 536 GLN cc_start: 0.8806 (mt0) cc_final: 0.8454 (tt0) REVERT: C 177 ARG cc_start: 0.6589 (mmm-85) cc_final: 0.6207 (mmm-85) REVERT: C 212 GLU cc_start: 0.7817 (tt0) cc_final: 0.7272 (tm-30) REVERT: C 360 GLU cc_start: 0.8096 (tt0) cc_final: 0.7771 (tt0) REVERT: C 361 GLU cc_start: 0.7924 (tt0) cc_final: 0.7386 (tm-30) REVERT: C 363 LYS cc_start: 0.8700 (tttt) cc_final: 0.8294 (ttmm) REVERT: C 389 PHE cc_start: 0.8330 (t80) cc_final: 0.7759 (t80) REVERT: C 399 VAL cc_start: 0.5461 (OUTLIER) cc_final: 0.4970 (m) REVERT: C 402 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 361 GLU cc_start: 0.8063 (tt0) cc_final: 0.6998 (tm-30) REVERT: D 406 TYR cc_start: 0.8816 (p90) cc_final: 0.8253 (p90) REVERT: D 447 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7497 (tt) REVERT: F 202 MET cc_start: 0.8606 (mmm) cc_final: 0.7882 (mtt) REVERT: F 387 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7744 (mmm-85) REVERT: F 512 MET cc_start: 0.8718 (mtm) cc_final: 0.8350 (mtm) REVERT: F 523 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8707 (p) REVERT: G 177 ARG cc_start: 0.7227 (mmm-85) cc_final: 0.6806 (mmm-85) REVERT: G 183 MET cc_start: 0.9129 (mtt) cc_final: 0.8523 (mtm) REVERT: G 202 MET cc_start: 0.8177 (mmm) cc_final: 0.7921 (mtp) REVERT: G 341 GLN cc_start: 0.8129 (mt0) cc_final: 0.7910 (mt0) REVERT: G 363 LYS cc_start: 0.9000 (tttt) cc_final: 0.8778 (ttmm) REVERT: G 424 MET cc_start: 0.9221 (mtm) cc_final: 0.8767 (mtm) REVERT: G 502 LYS cc_start: 0.8125 (mttt) cc_final: 0.7824 (mtmm) REVERT: H 177 ARG cc_start: 0.7415 (ttp80) cc_final: 0.6780 (ttm-80) REVERT: H 183 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8307 (ptp) REVERT: H 201 LYS cc_start: 0.9114 (mttm) cc_final: 0.8810 (mtpp) REVERT: H 212 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7186 (tm-30) REVERT: H 427 ASP cc_start: 0.8491 (m-30) cc_final: 0.8082 (m-30) REVERT: H 447 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7877 (tt) REVERT: H 478 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (p) REVERT: I 212 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8258 (tm-30) REVERT: I 293 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7898 (tp) REVERT: I 319 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7847 (tm-30) REVERT: I 382 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8747 (tt) REVERT: I 389 PHE cc_start: 0.8337 (t80) cc_final: 0.7993 (t80) REVERT: I 447 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7931 (tp) REVERT: I 496 LEU cc_start: 0.9110 (mp) cc_final: 0.8753 (tp) REVERT: I 512 MET cc_start: 0.8845 (mtm) cc_final: 0.8477 (mtt) REVERT: I 550 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8895 (p) REVERT: J 200 GLN cc_start: 0.8114 (pt0) cc_final: 0.7511 (pt0) REVERT: J 304 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.8990 (p) REVERT: K 197 LEU cc_start: 0.8268 (mp) cc_final: 0.7959 (mp) REVERT: K 212 GLU cc_start: 0.8527 (tt0) cc_final: 0.8267 (tt0) REVERT: K 429 GLU cc_start: 0.8557 (tt0) cc_final: 0.8219 (tt0) REVERT: K 454 LEU cc_start: 0.8802 (mt) cc_final: 0.8569 (mp) REVERT: K 469 VAL cc_start: 0.9323 (t) cc_final: 0.8996 (p) REVERT: K 482 GLN cc_start: 0.8464 (mt0) cc_final: 0.8115 (mt0) REVERT: K 536 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8952 (mt0) REVERT: L 177 ARG cc_start: 0.6969 (mmm-85) cc_final: 0.6132 (ttt-90) REVERT: L 305 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: L 363 LYS cc_start: 0.8934 (tttt) cc_final: 0.8361 (mtpp) REVERT: L 447 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7686 (tt) REVERT: L 473 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8721 (m) REVERT: L 512 MET cc_start: 0.8975 (mtm) cc_final: 0.8375 (mtp) REVERT: L 540 TRP cc_start: 0.8398 (t60) cc_final: 0.8117 (t60) REVERT: L 556 ARG cc_start: 0.6738 (ttm170) cc_final: 0.6330 (tpp-160) REVERT: M 177 ARG cc_start: 0.7004 (mtp85) cc_final: 0.6105 (mtp85) REVERT: M 285 GLU cc_start: 0.7833 (tp30) cc_final: 0.7470 (tm-30) REVERT: M 447 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7342 (tp) REVERT: N 212 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7697 (tm-30) REVERT: N 289 PHE cc_start: 0.8116 (t80) cc_final: 0.7750 (t80) REVERT: N 341 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: N 360 GLU cc_start: 0.7897 (tt0) cc_final: 0.7382 (tt0) REVERT: N 363 LYS cc_start: 0.8864 (tttt) cc_final: 0.8409 (ttmt) REVERT: N 410 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8475 (mm) REVERT: N 523 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8738 (p) REVERT: O 200 GLN cc_start: 0.7478 (pt0) cc_final: 0.6693 (pt0) REVERT: O 274 ASP cc_start: 0.8892 (t0) cc_final: 0.8219 (t0) REVERT: O 285 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7444 (tm-30) REVERT: O 482 GLN cc_start: 0.8379 (mt0) cc_final: 0.7731 (mt0) REVERT: O 486 PHE cc_start: 0.8421 (t80) cc_final: 0.8159 (t80) REVERT: O 540 TRP cc_start: 0.8128 (t60) cc_final: 0.7500 (t-100) REVERT: P 319 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7924 (tm-30) REVERT: P 360 GLU cc_start: 0.8128 (tt0) cc_final: 0.7889 (tt0) REVERT: P 409 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: P 410 ILE cc_start: 0.9028 (mt) cc_final: 0.8545 (tt) REVERT: P 427 ASP cc_start: 0.8023 (m-30) cc_final: 0.7616 (m-30) REVERT: P 510 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (m) REVERT: P 540 TRP cc_start: 0.8882 (t60) cc_final: 0.8487 (t60) outliers start: 180 outliers final: 141 residues processed: 482 average time/residue: 0.2291 time to fit residues: 187.3324 Evaluate side-chains 474 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 311 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 480 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 397 ARG Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 394 ILE Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain K residue 536 GLN Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 305 GLU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 513 ILE Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 366 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 397 ARG Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 409 MET Chi-restraints excluded: chain P residue 412 VAL Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 478 THR Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 533 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 306 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 474 optimal weight: 0.2980 chunk 196 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 ASN I 341 GLN J 432 ASN K 341 GLN K 432 ASN K 536 GLN L 421 GLN L 432 ASN ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.082719 restraints weight = 55996.361| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.08 r_work: 0.2768 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 40995 Z= 0.235 Angle : 0.632 11.274 55470 Z= 0.335 Chirality : 0.047 0.185 6525 Planarity : 0.005 0.085 7035 Dihedral : 6.047 59.541 5925 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.93 % Allowed : 15.16 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.11), residues: 5115 helix: -1.30 (0.20), residues: 675 sheet: 0.27 (0.10), residues: 2685 loop : -2.20 (0.12), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 397 TYR 0.016 0.002 TYR M 195 PHE 0.025 0.002 PHE M 289 TRP 0.011 0.001 TRP O 309 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00577 (40995) covalent geometry : angle 0.63184 (55470) hydrogen bonds : bond 0.04963 ( 2056) hydrogen bonds : angle 5.14937 ( 5712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 304 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 GLU cc_start: 0.8112 (tt0) cc_final: 0.7724 (tt0) REVERT: A 389 PHE cc_start: 0.8189 (t80) cc_final: 0.7914 (t80) REVERT: A 409 MET cc_start: 0.8749 (ttp) cc_final: 0.8517 (ttm) REVERT: A 555 ASP cc_start: 0.7597 (m-30) cc_final: 0.7189 (m-30) REVERT: B 427 ASP cc_start: 0.8307 (m-30) cc_final: 0.8004 (t0) REVERT: B 523 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9136 (p) REVERT: B 536 GLN cc_start: 0.8824 (mt0) cc_final: 0.8492 (tt0) REVERT: C 177 ARG cc_start: 0.6548 (mmm-85) cc_final: 0.6173 (mmm-85) REVERT: C 212 GLU cc_start: 0.7921 (tt0) cc_final: 0.7316 (tm-30) REVERT: C 360 GLU cc_start: 0.8203 (tt0) cc_final: 0.7819 (tt0) REVERT: C 361 GLU cc_start: 0.7948 (tt0) cc_final: 0.7486 (tm-30) REVERT: C 389 PHE cc_start: 0.8231 (t80) cc_final: 0.7785 (t80) REVERT: C 402 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 361 GLU cc_start: 0.8035 (tt0) cc_final: 0.7029 (tm-30) REVERT: D 406 TYR cc_start: 0.8818 (p90) cc_final: 0.8272 (p90) REVERT: D 432 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7742 (p0) REVERT: D 447 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7487 (tt) REVERT: F 177 ARG cc_start: 0.6473 (mtp85) cc_final: 0.6079 (mtp85) REVERT: F 202 MET cc_start: 0.8529 (mmm) cc_final: 0.7875 (mtt) REVERT: F 449 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: F 512 MET cc_start: 0.8748 (mtm) cc_final: 0.8449 (mtm) REVERT: G 177 ARG cc_start: 0.7183 (mmm-85) cc_final: 0.6876 (mmm-85) REVERT: G 183 MET cc_start: 0.9123 (mtt) cc_final: 0.8637 (mtm) REVERT: G 202 MET cc_start: 0.8257 (mmm) cc_final: 0.7584 (mmm) REVERT: G 212 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8022 (tt0) REVERT: G 424 MET cc_start: 0.9215 (mtm) cc_final: 0.8782 (mtm) REVERT: G 502 LYS cc_start: 0.8131 (mttt) cc_final: 0.7814 (mtmm) REVERT: H 177 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6836 (ttm-80) REVERT: H 183 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8396 (ptp) REVERT: H 201 LYS cc_start: 0.9136 (mttm) cc_final: 0.8833 (mtpp) REVERT: H 212 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7192 (tm-30) REVERT: H 402 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7858 (mm-30) REVERT: H 427 ASP cc_start: 0.8514 (m-30) cc_final: 0.8045 (m-30) REVERT: H 447 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7869 (tt) REVERT: I 212 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8315 (tm-30) REVERT: I 293 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7893 (tp) REVERT: I 382 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8766 (tt) REVERT: I 389 PHE cc_start: 0.8319 (t80) cc_final: 0.8050 (t80) REVERT: I 447 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7737 (tp) REVERT: I 496 LEU cc_start: 0.8948 (mp) cc_final: 0.8663 (tp) REVERT: I 512 MET cc_start: 0.8962 (mtm) cc_final: 0.8599 (mtt) REVERT: I 550 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8907 (p) REVERT: J 200 GLN cc_start: 0.8218 (pt0) cc_final: 0.7621 (pt0) REVERT: J 304 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8998 (p) REVERT: K 197 LEU cc_start: 0.8140 (mp) cc_final: 0.7813 (mp) REVERT: K 212 GLU cc_start: 0.8579 (tt0) cc_final: 0.8326 (tt0) REVERT: K 429 GLU cc_start: 0.8554 (tt0) cc_final: 0.8235 (tt0) REVERT: K 482 GLN cc_start: 0.8397 (mt0) cc_final: 0.8051 (mt0) REVERT: K 536 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8552 (mt0) REVERT: L 177 ARG cc_start: 0.6874 (mmm-85) cc_final: 0.6096 (ttt-90) REVERT: L 305 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: L 363 LYS cc_start: 0.8983 (tttt) cc_final: 0.8359 (mtpp) REVERT: L 447 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7736 (tt) REVERT: L 540 TRP cc_start: 0.8382 (t60) cc_final: 0.8106 (t60) REVERT: L 556 ARG cc_start: 0.6759 (ttm170) cc_final: 0.6371 (tpp-160) REVERT: M 177 ARG cc_start: 0.6923 (mtp85) cc_final: 0.6062 (ttt-90) REVERT: M 285 GLU cc_start: 0.7843 (tp30) cc_final: 0.7368 (tm-30) REVERT: M 447 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7539 (tp) REVERT: M 473 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8720 (m) REVERT: N 212 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7694 (tm-30) REVERT: N 341 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: N 360 GLU cc_start: 0.7949 (tt0) cc_final: 0.7439 (tt0) REVERT: N 363 LYS cc_start: 0.8903 (tttt) cc_final: 0.8440 (ttmt) REVERT: N 410 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8449 (mm) REVERT: N 523 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8764 (p) REVERT: O 200 GLN cc_start: 0.7591 (pt0) cc_final: 0.6790 (pt0) REVERT: O 274 ASP cc_start: 0.8847 (t0) cc_final: 0.8157 (t0) REVERT: O 482 GLN cc_start: 0.8577 (mt0) cc_final: 0.7943 (mt0) REVERT: O 486 PHE cc_start: 0.8407 (t80) cc_final: 0.8153 (t80) REVERT: O 540 TRP cc_start: 0.8102 (t60) cc_final: 0.7427 (t-100) REVERT: P 360 GLU cc_start: 0.8127 (tt0) cc_final: 0.7868 (tt0) REVERT: P 409 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7871 (ttp) REVERT: P 410 ILE cc_start: 0.9043 (mt) cc_final: 0.8519 (tt) REVERT: P 510 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8645 (m) REVERT: P 540 TRP cc_start: 0.8904 (t60) cc_final: 0.8457 (t60) outliers start: 218 outliers final: 173 residues processed: 489 average time/residue: 0.2229 time to fit residues: 185.6898 Evaluate side-chains 492 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 298 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 466 SER Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 378 ASN Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 341 GLN Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 444 VAL Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 312 ASP Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 394 ILE Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 432 ASN Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain K residue 536 GLN Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 305 GLU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 432 ASN Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 419 ASP Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 513 ILE Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 366 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 397 ARG Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 409 MET Chi-restraints excluded: chain P residue 412 VAL Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 478 THR Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 428 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 461 optimal weight: 4.9990 chunk 436 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN K 536 GLN O 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.083946 restraints weight = 56427.803| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.05 r_work: 0.2784 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40995 Z= 0.173 Angle : 0.587 10.901 55470 Z= 0.312 Chirality : 0.045 0.168 6525 Planarity : 0.005 0.081 7035 Dihedral : 5.828 56.279 5925 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.63 % Allowed : 15.53 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.12), residues: 5115 helix: -1.27 (0.20), residues: 705 sheet: 0.33 (0.10), residues: 2685 loop : -2.22 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG I 397 TYR 0.011 0.001 TYR M 195 PHE 0.041 0.002 PHE F 289 TRP 0.011 0.001 TRP F 309 HIS 0.002 0.001 HIS P 303 Details of bonding type rmsd covalent geometry : bond 0.00422 (40995) covalent geometry : angle 0.58689 (55470) hydrogen bonds : bond 0.04388 ( 2056) hydrogen bonds : angle 4.96906 ( 5712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 314 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 GLU cc_start: 0.8090 (tt0) cc_final: 0.7702 (tt0) REVERT: A 389 PHE cc_start: 0.8126 (t80) cc_final: 0.7857 (t80) REVERT: A 409 MET cc_start: 0.8682 (ttp) cc_final: 0.8473 (ttm) REVERT: A 555 ASP cc_start: 0.7548 (m-30) cc_final: 0.7103 (m-30) REVERT: B 212 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 427 ASP cc_start: 0.8300 (m-30) cc_final: 0.7998 (t0) REVERT: B 473 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8945 (m) REVERT: B 523 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9140 (p) REVERT: B 536 GLN cc_start: 0.8822 (mt0) cc_final: 0.8478 (tt0) REVERT: C 177 ARG cc_start: 0.6543 (mmm-85) cc_final: 0.6149 (mmm-85) REVERT: C 212 GLU cc_start: 0.7865 (tt0) cc_final: 0.7309 (tm-30) REVERT: C 360 GLU cc_start: 0.8170 (tt0) cc_final: 0.7774 (tt0) REVERT: C 361 GLU cc_start: 0.7943 (tt0) cc_final: 0.7420 (tm-30) REVERT: C 363 LYS cc_start: 0.8672 (tttt) cc_final: 0.8279 (ttmm) REVERT: C 402 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 361 GLU cc_start: 0.8057 (tt0) cc_final: 0.6993 (tm-30) REVERT: D 406 TYR cc_start: 0.8829 (p90) cc_final: 0.8291 (p90) REVERT: D 432 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7600 (p0) REVERT: D 447 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7539 (tt) REVERT: F 177 ARG cc_start: 0.6528 (mtp85) cc_final: 0.6102 (mtp85) REVERT: F 202 MET cc_start: 0.8502 (mmm) cc_final: 0.7915 (mtt) REVERT: F 387 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7754 (mmm-85) REVERT: F 473 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8576 (m) REVERT: F 512 MET cc_start: 0.8735 (mtm) cc_final: 0.8382 (mtm) REVERT: F 523 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8683 (p) REVERT: G 177 ARG cc_start: 0.7235 (mmm-85) cc_final: 0.6823 (mmm-85) REVERT: G 183 MET cc_start: 0.9117 (mtt) cc_final: 0.8545 (mtm) REVERT: G 202 MET cc_start: 0.8243 (mmm) cc_final: 0.7568 (mmm) REVERT: G 212 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8027 (tt0) REVERT: G 289 PHE cc_start: 0.8163 (t80) cc_final: 0.7656 (t80) REVERT: G 424 MET cc_start: 0.9236 (mtm) cc_final: 0.8788 (mtm) REVERT: G 502 LYS cc_start: 0.8128 (mttt) cc_final: 0.7824 (mtmm) REVERT: H 177 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6829 (ttm-80) REVERT: H 183 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8324 (ptp) REVERT: H 201 LYS cc_start: 0.9127 (mttm) cc_final: 0.8823 (mtpp) REVERT: H 212 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7206 (tm-30) REVERT: H 402 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7836 (mm-30) REVERT: H 427 ASP cc_start: 0.8489 (m-30) cc_final: 0.8063 (m-30) REVERT: H 447 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7872 (tt) REVERT: I 212 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8266 (tm-30) REVERT: I 293 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7871 (tp) REVERT: I 319 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7851 (tm-30) REVERT: I 382 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8765 (tt) REVERT: I 389 PHE cc_start: 0.8335 (t80) cc_final: 0.8080 (t80) REVERT: I 447 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7719 (tp) REVERT: I 496 LEU cc_start: 0.9132 (mp) cc_final: 0.8766 (tp) REVERT: I 512 MET cc_start: 0.8930 (mtm) cc_final: 0.8575 (mtt) REVERT: I 550 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8918 (p) REVERT: J 200 GLN cc_start: 0.7992 (pt0) cc_final: 0.7465 (pt0) REVERT: J 304 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8994 (p) REVERT: K 197 LEU cc_start: 0.8218 (mp) cc_final: 0.7894 (mp) REVERT: K 212 GLU cc_start: 0.8521 (tt0) cc_final: 0.8269 (tt0) REVERT: K 305 GLU cc_start: 0.8034 (tt0) cc_final: 0.7769 (tt0) REVERT: K 429 GLU cc_start: 0.8511 (tt0) cc_final: 0.8208 (tt0) REVERT: K 469 VAL cc_start: 0.9333 (t) cc_final: 0.9025 (p) REVERT: K 482 GLN cc_start: 0.8406 (mt0) cc_final: 0.8061 (mt0) REVERT: L 177 ARG cc_start: 0.6883 (mmm-85) cc_final: 0.6128 (ttt-90) REVERT: L 305 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: L 363 LYS cc_start: 0.8980 (tttt) cc_final: 0.8387 (mtpp) REVERT: L 447 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7691 (tt) REVERT: L 540 TRP cc_start: 0.8410 (t60) cc_final: 0.8122 (t60) REVERT: L 556 ARG cc_start: 0.6779 (ttm170) cc_final: 0.6383 (tpp-160) REVERT: M 177 ARG cc_start: 0.6973 (mtp85) cc_final: 0.6069 (ttt-90) REVERT: M 200 GLN cc_start: 0.8088 (pt0) cc_final: 0.7749 (pt0) REVERT: M 285 GLU cc_start: 0.7860 (tp30) cc_final: 0.7490 (tm-30) REVERT: M 447 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7473 (tp) REVERT: M 473 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8873 (m) REVERT: N 212 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7715 (tm-30) REVERT: N 289 PHE cc_start: 0.8103 (t80) cc_final: 0.7707 (t80) REVERT: N 360 GLU cc_start: 0.7889 (tt0) cc_final: 0.7386 (tt0) REVERT: N 363 LYS cc_start: 0.8861 (tttt) cc_final: 0.8629 (ttmt) REVERT: N 410 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8467 (mm) REVERT: N 523 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8762 (p) REVERT: O 200 GLN cc_start: 0.7586 (pt0) cc_final: 0.6761 (pt0) REVERT: O 274 ASP cc_start: 0.8879 (t0) cc_final: 0.8203 (t0) REVERT: O 482 GLN cc_start: 0.8586 (mt0) cc_final: 0.7925 (mt0) REVERT: O 486 PHE cc_start: 0.8441 (t80) cc_final: 0.8197 (t80) REVERT: O 540 TRP cc_start: 0.8130 (t60) cc_final: 0.7474 (t-100) REVERT: P 341 GLN cc_start: 0.8140 (mt0) cc_final: 0.7822 (mt0) REVERT: P 360 GLU cc_start: 0.8124 (tt0) cc_final: 0.7885 (tt0) REVERT: P 409 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7838 (ttp) REVERT: P 410 ILE cc_start: 0.9045 (mt) cc_final: 0.8522 (tt) REVERT: P 411 ARG cc_start: 0.8659 (ttp-170) cc_final: 0.8399 (ttp80) REVERT: P 510 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8551 (m) REVERT: P 540 TRP cc_start: 0.8899 (t60) cc_final: 0.8453 (t60) outliers start: 205 outliers final: 170 residues processed: 488 average time/residue: 0.2297 time to fit residues: 190.4648 Evaluate side-chains 500 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 309 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 466 SER Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 378 ASN Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 480 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 341 GLN Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 444 VAL Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 394 ILE Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 274 ASP Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 305 GLU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain O residue 389 PHE Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 513 ILE Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 366 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 397 ARG Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 409 MET Chi-restraints excluded: chain P residue 412 VAL Chi-restraints excluded: chain P residue 473 THR Chi-restraints excluded: chain P residue 478 THR Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 324 optimal weight: 0.0010 chunk 336 optimal weight: 0.2980 chunk 9 optimal weight: 4.9990 chunk 295 optimal weight: 0.0670 chunk 320 optimal weight: 3.9990 overall best weight: 0.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 432 ASN B 432 ASN H 421 GLN H 506 ASN J 432 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 536 GLN L 421 GLN L 432 ASN M 482 GLN ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.089252 restraints weight = 55183.874| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40995 Z= 0.093 Angle : 0.524 11.229 55470 Z= 0.277 Chirality : 0.044 0.149 6525 Planarity : 0.005 0.074 7035 Dihedral : 5.118 54.243 5925 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.55 % Allowed : 17.65 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 5115 helix: -1.15 (0.20), residues: 765 sheet: 0.52 (0.10), residues: 2745 loop : -2.30 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 397 TYR 0.015 0.001 TYR P 195 PHE 0.028 0.001 PHE M 289 TRP 0.012 0.001 TRP F 309 HIS 0.001 0.000 HIS M 288 Details of bonding type rmsd covalent geometry : bond 0.00212 (40995) covalent geometry : angle 0.52363 (55470) hydrogen bonds : bond 0.03151 ( 2056) hydrogen bonds : angle 4.43189 ( 5712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 364 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.7612 (pt0) cc_final: 0.7326 (pt0) REVERT: A 361 GLU cc_start: 0.8086 (tt0) cc_final: 0.7865 (tt0) REVERT: A 363 LYS cc_start: 0.8835 (tttt) cc_final: 0.8333 (ttmm) REVERT: A 389 PHE cc_start: 0.8140 (t80) cc_final: 0.7836 (t80) REVERT: A 409 MET cc_start: 0.8541 (ttp) cc_final: 0.8310 (ttm) REVERT: A 555 ASP cc_start: 0.7768 (m-30) cc_final: 0.7183 (t0) REVERT: B 212 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 389 PHE cc_start: 0.8109 (t80) cc_final: 0.7774 (t80) REVERT: B 513 ILE cc_start: 0.9027 (mm) cc_final: 0.8801 (pt) REVERT: B 536 GLN cc_start: 0.8724 (mt0) cc_final: 0.8366 (tt0) REVERT: C 212 GLU cc_start: 0.7889 (tt0) cc_final: 0.7474 (tm-30) REVERT: C 289 PHE cc_start: 0.7851 (t80) cc_final: 0.7605 (t80) REVERT: C 360 GLU cc_start: 0.8077 (tt0) cc_final: 0.7767 (tt0) REVERT: C 361 GLU cc_start: 0.8052 (tt0) cc_final: 0.7410 (tm-30) REVERT: C 363 LYS cc_start: 0.8762 (tttt) cc_final: 0.8358 (ttmm) REVERT: C 402 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7385 (mm-30) REVERT: C 530 VAL cc_start: 0.8899 (t) cc_final: 0.8614 (m) REVERT: D 307 SER cc_start: 0.9270 (t) cc_final: 0.8887 (p) REVERT: D 361 GLU cc_start: 0.8080 (tt0) cc_final: 0.7020 (tm-30) REVERT: D 406 TYR cc_start: 0.8734 (p90) cc_final: 0.8205 (p90) REVERT: D 447 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7516 (tt) REVERT: D 513 ILE cc_start: 0.9556 (mm) cc_final: 0.9249 (mm) REVERT: F 177 ARG cc_start: 0.6512 (mtp85) cc_final: 0.6154 (mtp85) REVERT: F 202 MET cc_start: 0.8427 (mmm) cc_final: 0.7818 (mtt) REVERT: F 387 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7854 (mmm-85) REVERT: G 177 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.6761 (mmm-85) REVERT: G 183 MET cc_start: 0.9188 (mtt) cc_final: 0.8635 (mtm) REVERT: G 405 THR cc_start: 0.9402 (m) cc_final: 0.9117 (p) REVERT: G 424 MET cc_start: 0.9027 (mtm) cc_final: 0.8709 (mtm) REVERT: G 502 LYS cc_start: 0.8456 (mttt) cc_final: 0.8170 (mtmt) REVERT: H 177 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6709 (ttm-80) REVERT: H 212 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7048 (tm-30) REVERT: H 402 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7977 (mm-30) REVERT: H 410 ILE cc_start: 0.9225 (mt) cc_final: 0.9015 (mm) REVERT: H 447 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7882 (tt) REVERT: H 496 LEU cc_start: 0.9072 (mp) cc_final: 0.8762 (mp) REVERT: I 212 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8169 (tm-30) REVERT: I 319 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7762 (tm-30) REVERT: I 363 LYS cc_start: 0.8791 (tttt) cc_final: 0.8517 (ttmm) REVERT: I 382 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8515 (tt) REVERT: I 389 PHE cc_start: 0.8137 (t80) cc_final: 0.7828 (t80) REVERT: I 447 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7826 (tp) REVERT: I 496 LEU cc_start: 0.9060 (mp) cc_final: 0.8687 (tp) REVERT: I 512 MET cc_start: 0.8809 (mtm) cc_final: 0.8436 (mtt) REVERT: I 550 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8684 (p) REVERT: J 200 GLN cc_start: 0.7837 (pt0) cc_final: 0.7405 (pt0) REVERT: J 272 TYR cc_start: 0.8641 (t80) cc_final: 0.8194 (t80) REVERT: J 304 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8936 (p) REVERT: K 212 GLU cc_start: 0.8507 (tt0) cc_final: 0.8246 (tt0) REVERT: K 429 GLU cc_start: 0.8535 (tt0) cc_final: 0.8208 (tt0) REVERT: K 454 LEU cc_start: 0.8793 (mt) cc_final: 0.8545 (mp) REVERT: K 469 VAL cc_start: 0.9198 (t) cc_final: 0.8941 (p) REVERT: K 482 GLN cc_start: 0.8431 (mt0) cc_final: 0.8205 (mt0) REVERT: L 177 ARG cc_start: 0.6905 (mmm-85) cc_final: 0.6156 (ttt180) REVERT: L 363 LYS cc_start: 0.8863 (tttt) cc_final: 0.8300 (mtpp) REVERT: L 447 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7665 (tt) REVERT: L 540 TRP cc_start: 0.8362 (t60) cc_final: 0.8125 (t60) REVERT: M 177 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6071 (ttt-90) REVERT: M 285 GLU cc_start: 0.7622 (tp30) cc_final: 0.7365 (tm-30) REVERT: M 409 MET cc_start: 0.8302 (tmm) cc_final: 0.7334 (ttm) REVERT: M 447 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7292 (tp) REVERT: N 177 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6948 (ttt-90) REVERT: N 212 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7510 (tm-30) REVERT: N 289 PHE cc_start: 0.7949 (t80) cc_final: 0.7563 (t80) REVERT: N 360 GLU cc_start: 0.7769 (tt0) cc_final: 0.7242 (tt0) REVERT: N 410 ILE cc_start: 0.8911 (mt) cc_final: 0.8699 (mm) REVERT: N 523 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8724 (p) REVERT: O 274 ASP cc_start: 0.8962 (t0) cc_final: 0.8251 (t0) REVERT: O 285 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7436 (tm-30) REVERT: O 482 GLN cc_start: 0.8306 (mt0) cc_final: 0.7836 (mt0) REVERT: O 486 PHE cc_start: 0.8394 (t80) cc_final: 0.8151 (t80) REVERT: O 513 ILE cc_start: 0.9232 (mm) cc_final: 0.8694 (pt) REVERT: O 540 TRP cc_start: 0.8055 (t60) cc_final: 0.7422 (t-100) REVERT: P 319 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7945 (tm-30) REVERT: P 360 GLU cc_start: 0.7962 (tt0) cc_final: 0.7412 (mt-10) REVERT: P 409 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8010 (ttp) REVERT: P 410 ILE cc_start: 0.9001 (mt) cc_final: 0.8555 (tt) REVERT: P 427 ASP cc_start: 0.8259 (m-30) cc_final: 0.7946 (m-30) REVERT: P 540 TRP cc_start: 0.8801 (t60) cc_final: 0.8418 (t60) outliers start: 113 outliers final: 72 residues processed: 459 average time/residue: 0.2347 time to fit residues: 181.1277 Evaluate side-chains 416 residues out of total 4470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 333 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 382 ILE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 444 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 409 MET Chi-restraints excluded: chain P residue 412 VAL Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 193 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 173 optimal weight: 0.0170 chunk 310 optimal weight: 3.9990 chunk 275 optimal weight: 0.1980 chunk 427 optimal weight: 0.7980 chunk 277 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 463 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 200 GLN B 432 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 536 GLN ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 482 GLN ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.090101 restraints weight = 55476.975| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.00 r_work: 0.2871 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 40995 Z= 0.128 Angle : 0.625 59.200 55470 Z= 0.351 Chirality : 0.045 0.270 6525 Planarity : 0.005 0.073 7035 Dihedral : 5.117 54.231 5925 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.26 % Allowed : 18.06 % Favored : 79.68 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 5115 helix: -1.14 (0.20), residues: 765 sheet: 0.54 (0.10), residues: 2745 loop : -2.29 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.000 ARG P 397 TYR 0.011 0.001 TYR F 195 PHE 0.027 0.001 PHE M 289 TRP 0.010 0.001 TRP F 309 HIS 0.001 0.000 HIS M 288 Details of bonding type rmsd covalent geometry : bond 0.00292 (40995) covalent geometry : angle 0.62465 (55470) hydrogen bonds : bond 0.03162 ( 2056) hydrogen bonds : angle 4.43397 ( 5712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8126.69 seconds wall clock time: 140 minutes 43.81 seconds (8443.81 seconds total)