Starting phenix.real_space_refine on Tue May 20 07:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8say_40284/05_2025/8say_40284_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8say_40284/05_2025/8say_40284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8say_40284/05_2025/8say_40284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8say_40284/05_2025/8say_40284.map" model { file = "/net/cci-nas-00/data/ceres_data/8say_40284/05_2025/8say_40284_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8say_40284/05_2025/8say_40284_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 129 5.16 5 C 12429 2.51 5 N 3323 2.21 5 O 4021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19902 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "C" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "M" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.29, per 1000 atoms: 0.62 Number of scatterers: 19902 At special positions: 0 Unit cell: (157.768, 159.9, 139.646, 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 129 16.00 O 4021 8.00 N 3323 7.00 C 12429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.05 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.02 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.04 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.05 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.04 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 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN J 10 " - " MAN J 11 " " MAN O 4 " - " MAN O 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " " MAN V 10 " - " MAN V 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA T 3 " - " MAN T 5 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 10 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 2.6 seconds 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4552 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 49 sheets defined 18.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.175A pdb=" N GLU A 62 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.768A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.614A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.509A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.506A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 579 removed outlier: 3.823A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 4.927A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 3.731A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN B 616 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 611 through 616' Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.695A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 5.622A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 removed outlier: 4.341A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 58 through 63 removed outlier: 4.240A pdb=" N GLU F 62 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 63 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 99 through 116 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 334 through 350 removed outlier: 3.734A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 3.537A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 535 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 571 through 579 Processing helix chain 'G' and resid 580 through 596 removed outlier: 5.017A pdb=" N LEU G 587 " --> pdb=" O VAL G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 616 removed outlier: 3.658A pdb=" N SER G 615 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN G 616 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 616' Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.663A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP G 623 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 5.281A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 662 removed outlier: 3.503A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS G 655 " --> pdb=" O ASN G 651 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU G 657 " --> pdb=" O GLN G 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 57 through 61 removed outlier: 3.598A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR K 61 " --> pdb=" O ALA K 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 57 through 61' Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.845A pdb=" N ALA K 73 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 removed outlier: 3.564A pdb=" N SER K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 334 through 350 removed outlier: 3.681A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 474 through 481 removed outlier: 3.608A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 535 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 571 through 579 removed outlier: 3.810A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 596 removed outlier: 4.241A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG L 585 " --> pdb=" O LEU L 581 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU L 587 " --> pdb=" O VAL L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 616 removed outlier: 3.722A pdb=" N SER L 615 " --> pdb=" O ASN L 611 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN L 616 " --> pdb=" O SER L 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 611 through 616' Processing helix chain 'L' and resid 618 through 626 removed outlier: 3.992A pdb=" N ILE L 622 " --> pdb=" O ASN L 618 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRP L 623 " --> pdb=" O LEU L 619 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP L 624 " --> pdb=" O SER L 620 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET L 626 " --> pdb=" O ILE L 622 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 5.278A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 661 removed outlier: 4.287A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS L 655 " --> pdb=" O ASN L 651 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.966A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.801A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 5.432A pdb=" N ASN A 160 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR A 128 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 10.839A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.016A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 361 removed outlier: 3.547A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.623A pdb=" N SER C 124 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 123 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 57 " --> pdb=" O ASN C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 23 removed outlier: 3.646A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 240 through 241 removed outlier: 7.402A pdb=" N VAL D 240 " --> pdb=" O THR D 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 247 through 248 Processing sheet with id=AB7, first strand: chain 'D' and resid 251 through 253 Processing sheet with id=AB8, first strand: chain 'D' and resid 285 through 286 removed outlier: 3.691A pdb=" N TYR D 281 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN D 270 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN D 317 " --> pdb=" O GLN D 270 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AC1, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.937A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.761A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.596A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 176 removed outlier: 5.313A pdb=" N ASN F 160 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR F 128 " --> pdb=" O ASN F 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.520A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.738A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.084A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 10.930A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN F 417 " --> pdb=" O ASN F 386 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 272 through 273 removed outlier: 10.930A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.084A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'F' and resid 359 through 361 removed outlier: 3.672A pdb=" N GLY F 393 " --> pdb=" O TYR F 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.721A pdb=" N VAL H 123 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.721A pdb=" N VAL H 123 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.707A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 240 through 241 removed outlier: 7.421A pdb=" N VAL I 240 " --> pdb=" O THR I 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 247 through 253 Processing sheet with id=AD6, first strand: chain 'I' and resid 285 through 286 removed outlier: 3.678A pdb=" N TYR I 281 " --> pdb=" O LYS I 285 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN I 270 " --> pdb=" O ASN I 317 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN I 317 " --> pdb=" O GLN I 270 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR I 328 " --> pdb=" O THR I 324 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 494 through 498 removed outlier: 3.911A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 38 " --> pdb=" O CYS L 604 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 45 through 46 removed outlier: 4.179A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AE1, first strand: chain 'K' and resid 91 through 92 removed outlier: 3.649A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 170 through 176 removed outlier: 5.468A pdb=" N ASN K 160 " --> pdb=" O THR K 128 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR K 128 " --> pdb=" O ASN K 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.486A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 271 through 273 removed outlier: 3.732A pdb=" N VAL K 271 " --> pdb=" O HIS K 287 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN K 417 " --> pdb=" O ASN K 386 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 271 through 273 removed outlier: 3.732A pdb=" N VAL K 271 " --> pdb=" O HIS K 287 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.039A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.296A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AE7, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.610A pdb=" N GLY K 393 " --> pdb=" O TYR K 361 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.643A pdb=" N SER M 124 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL M 123 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG M 57 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.643A pdb=" N SER M 124 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL M 123 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER M 116 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 17 through 23 removed outlier: 3.675A pdb=" N THR M 71 " --> pdb=" O TYR M 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 240 through 241 removed outlier: 7.434A pdb=" N VAL N 240 " --> pdb=" O THR N 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'N' and resid 247 through 253 Processing sheet with id=AF4, first strand: chain 'N' and resid 285 through 286 removed outlier: 3.640A pdb=" N TYR N 281 " --> pdb=" O LYS N 285 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR N 328 " --> pdb=" O THR N 324 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1557 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: 6.76 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6298 1.35 - 1.48: 5362 1.48 - 1.61: 8481 1.61 - 1.74: 0 1.74 - 1.87: 174 Bond restraints: 20315 Sorted by residual: bond pdb=" C2 MAN J 5 " pdb=" O2 MAN J 5 " ideal model delta sigma weight residual 1.407 1.475 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C2 MAN V 5 " pdb=" O2 MAN V 5 " ideal model delta sigma weight residual 1.407 1.474 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C2 MAN O 5 " pdb=" O2 MAN O 5 " ideal model delta sigma weight residual 1.407 1.469 -0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" C2 MAN R 5 " pdb=" O2 MAN R 5 " ideal model delta sigma weight residual 1.407 1.464 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C2 MAN J 4 " pdb=" O2 MAN J 4 " ideal model delta sigma weight residual 1.407 1.462 -0.055 2.00e-02 2.50e+03 7.43e+00 ... (remaining 20310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 26843 2.73 - 5.46: 675 5.46 - 8.19: 93 8.19 - 10.92: 16 10.92 - 13.65: 1 Bond angle restraints: 27628 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.28 -10.58 1.80e+00 3.09e-01 3.45e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 132.12 -10.42 1.80e+00 3.09e-01 3.35e+01 angle pdb=" C VAL N 339 " pdb=" N LEU N 340 " pdb=" CA LEU N 340 " ideal model delta sigma weight residual 121.70 130.95 -9.25 1.80e+00 3.09e-01 2.64e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 130.69 -8.99 1.80e+00 3.09e-01 2.49e+01 angle pdb=" C VAL I 339 " pdb=" N LEU I 340 " pdb=" CA LEU I 340 " ideal model delta sigma weight residual 121.70 130.15 -8.45 1.80e+00 3.09e-01 2.20e+01 ... (remaining 27623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.55: 12169 22.55 - 45.10: 617 45.10 - 67.66: 83 67.66 - 90.21: 96 90.21 - 112.76: 38 Dihedral angle restraints: 13003 sinusoidal: 5909 harmonic: 7094 Sorted by residual: dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 179.79 -86.79 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -166.08 80.08 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS K 126 " pdb=" SG CYS K 126 " pdb=" SG CYS K 196 " pdb=" CB CYS K 196 " ideal model delta sinusoidal sigma weight residual -86.00 -163.93 77.93 1 1.00e+01 1.00e-02 7.59e+01 ... (remaining 13000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2754 0.067 - 0.135: 462 0.135 - 0.202: 75 0.202 - 0.270: 8 0.270 - 0.337: 7 Chirality restraints: 3306 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 3303 not shown) Planarity restraints: 3442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 582 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ALA B 582 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 582 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 583 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 62 " -0.174 9.50e-02 1.11e+02 7.84e-02 4.89e+00 pdb=" NE ARG C 62 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 62 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 62 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 62 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 111 " -0.023 2.00e-02 2.50e+03 1.50e-02 4.48e+00 pdb=" CG TYR C 111 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 111 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 111 " -0.003 2.00e-02 2.50e+03 ... (remaining 3439 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 129 2.57 - 3.15: 16199 3.15 - 3.73: 28683 3.73 - 4.32: 40891 4.32 - 4.90: 67662 Nonbonded interactions: 153564 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" O CYS G 604 " model vdw 1.984 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O CYS B 604 " model vdw 1.991 3.040 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR G 606 " model vdw 2.043 3.040 nonbonded pdb=" OG1 THR K 163 " pdb=" OE1 GLU K 164 " model vdw 2.050 3.040 nonbonded pdb=" OG SER A 256 " pdb=" O LEU A 259 " model vdw 2.056 3.040 ... (remaining 153559 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and (resid 32 through 415 or resid 417 through 505)) selection = (chain 'K' and (resid 32 through 415 or resid 417 through 505)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'U' selection = chain 'X' } 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: 0.560 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 47.320 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.006 0.068 20421 Z= 0.287 Angle : 1.084 18.407 27904 Z= 0.532 Chirality : 0.055 0.337 3306 Planarity : 0.006 0.078 3430 Dihedral : 16.665 112.759 8325 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.54 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2433 helix: -1.77 (0.25), residues: 348 sheet: -0.80 (0.21), residues: 526 loop : -1.60 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 101 HIS 0.005 0.001 HIS A 105 PHE 0.028 0.002 PHE K 382 TYR 0.035 0.002 TYR C 111 ARG 0.019 0.001 ARG C 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 12) link_NAG-ASN : angle 2.33399 ( 36) link_ALPHA1-6 : bond 0.01022 ( 7) link_ALPHA1-6 : angle 2.69613 ( 21) link_BETA1-4 : bond 0.00693 ( 22) link_BETA1-4 : angle 5.19336 ( 66) link_ALPHA1-2 : bond 0.01304 ( 13) link_ALPHA1-2 : angle 4.15534 ( 39) link_ALPHA1-3 : bond 0.01132 ( 10) link_ALPHA1-3 : angle 4.00407 ( 30) hydrogen bonds : bond 0.23463 ( 576) hydrogen bonds : angle 9.13049 ( 1557) SS BOND : bond 0.00709 ( 42) SS BOND : angle 2.09058 ( 84) covalent geometry : bond 0.00608 (20315) covalent geometry : angle 1.02736 (27628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.7861 (tt) cc_final: 0.7611 (tt) REVERT: A 114 GLN cc_start: 0.7162 (tt0) cc_final: 0.6865 (pt0) REVERT: A 434 MET cc_start: 0.7472 (ttp) cc_final: 0.7222 (ttm) REVERT: B 591 GLN cc_start: 0.8168 (tp40) cc_final: 0.7951 (tt0) REVERT: C 91 THR cc_start: 0.8131 (m) cc_final: 0.7826 (t) REVERT: D 298 LYS cc_start: 0.7682 (ttpp) cc_final: 0.6865 (tptt) REVERT: F 95 MET cc_start: 0.7760 (ttp) cc_final: 0.7347 (ttp) REVERT: F 108 ILE cc_start: 0.7988 (tt) cc_final: 0.7748 (tt) REVERT: F 113 ASP cc_start: 0.7931 (t70) cc_final: 0.7659 (t0) REVERT: F 434 MET cc_start: 0.8335 (ttp) cc_final: 0.8061 (ttm) REVERT: G 610 TRP cc_start: 0.6838 (t-100) cc_final: 0.6621 (m100) REVERT: H 91 THR cc_start: 0.7818 (m) cc_final: 0.7479 (t) REVERT: I 298 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7322 (tttp) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.3294 time to fit residues: 273.7987 Evaluate side-chains 324 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 246 GLN A 300 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN C 52 ASN F 105 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN G 540 GLN G 590 GLN G 653 GLN H 3 GLN H 6 GLN H 77 ASN K 300 ASN L 650 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.203634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180208 restraints weight = 30004.715| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.33 r_work: 0.4045 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20421 Z= 0.164 Angle : 0.811 11.813 27904 Z= 0.403 Chirality : 0.050 0.214 3306 Planarity : 0.005 0.062 3430 Dihedral : 12.036 80.596 3905 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.84 % Favored : 93.92 % Rotamer: Outliers : 2.34 % Allowed : 10.35 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2433 helix: -1.27 (0.25), residues: 390 sheet: -0.29 (0.21), residues: 534 loop : -1.62 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 112 HIS 0.007 0.001 HIS A 66 PHE 0.027 0.002 PHE K 391 TYR 0.027 0.002 TYR H 111 ARG 0.007 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 1.86256 ( 36) link_ALPHA1-6 : bond 0.00443 ( 7) link_ALPHA1-6 : angle 1.41672 ( 21) link_BETA1-4 : bond 0.00606 ( 22) link_BETA1-4 : angle 3.63039 ( 66) link_ALPHA1-2 : bond 0.00771 ( 13) link_ALPHA1-2 : angle 1.92970 ( 39) link_ALPHA1-3 : bond 0.01249 ( 10) link_ALPHA1-3 : angle 2.31530 ( 30) hydrogen bonds : bond 0.05293 ( 576) hydrogen bonds : angle 6.34777 ( 1557) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.10720 ( 84) covalent geometry : bond 0.00365 (20315) covalent geometry : angle 0.78209 (27628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8117 (tt) cc_final: 0.7909 (tt) REVERT: A 207 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7373 (tptt) REVERT: B 530 MET cc_start: 0.7332 (mmm) cc_final: 0.6762 (mmm) REVERT: B 589 ASP cc_start: 0.8268 (m-30) cc_final: 0.7956 (m-30) REVERT: B 652 GLN cc_start: 0.6884 (tm-30) cc_final: 0.6590 (tm-30) REVERT: D 298 LYS cc_start: 0.7797 (ttpp) cc_final: 0.6955 (tttt) REVERT: F 95 MET cc_start: 0.7921 (ttp) cc_final: 0.7641 (ttp) REVERT: F 108 ILE cc_start: 0.8185 (tt) cc_final: 0.7958 (tt) REVERT: F 345 VAL cc_start: 0.8557 (t) cc_final: 0.8216 (t) REVERT: G 540 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: G 614 TRP cc_start: 0.4698 (m-10) cc_final: 0.3924 (m-10) REVERT: G 622 ILE cc_start: 0.6701 (mm) cc_final: 0.6370 (pt) REVERT: G 648 GLU cc_start: 0.7454 (pt0) cc_final: 0.7217 (mm-30) REVERT: G 659 ASP cc_start: 0.7786 (m-30) cc_final: 0.7549 (m-30) REVERT: I 298 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7338 (tttp) REVERT: K 69 TRP cc_start: 0.4312 (p-90) cc_final: 0.3633 (p-90) REVERT: K 114 GLN cc_start: 0.6844 (tt0) cc_final: 0.6583 (pt0) REVERT: K 211 GLU cc_start: 0.8085 (pm20) cc_final: 0.7868 (tt0) REVERT: L 540 GLN cc_start: 0.8069 (mt0) cc_final: 0.7729 (mt0) REVERT: L 610 TRP cc_start: 0.7522 (t-100) cc_final: 0.6652 (t-100) REVERT: M 58 THR cc_start: 0.8954 (m) cc_final: 0.8677 (t) REVERT: N 298 LYS cc_start: 0.7795 (ttpp) cc_final: 0.6965 (ttmm) outliers start: 50 outliers final: 34 residues processed: 383 average time/residue: 0.3185 time to fit residues: 184.8793 Evaluate side-chains 319 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 577 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 77 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN G 650 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN N 301 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.192734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166701 restraints weight = 29474.909| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.37 r_work: 0.3880 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20421 Z= 0.259 Angle : 0.895 15.076 27904 Z= 0.444 Chirality : 0.051 0.273 3306 Planarity : 0.005 0.049 3430 Dihedral : 10.992 83.334 3905 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.58 % Favored : 92.97 % Rotamer: Outliers : 3.65 % Allowed : 13.54 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2433 helix: -1.48 (0.24), residues: 418 sheet: -0.29 (0.22), residues: 512 loop : -1.82 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 112 HIS 0.006 0.002 HIS F 287 PHE 0.017 0.003 PHE D 319 TYR 0.053 0.003 TYR C 111 ARG 0.006 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 12) link_NAG-ASN : angle 2.11996 ( 36) link_ALPHA1-6 : bond 0.00401 ( 7) link_ALPHA1-6 : angle 1.62393 ( 21) link_BETA1-4 : bond 0.00578 ( 22) link_BETA1-4 : angle 3.29511 ( 66) link_ALPHA1-2 : bond 0.00856 ( 13) link_ALPHA1-2 : angle 1.76330 ( 39) link_ALPHA1-3 : bond 0.01103 ( 10) link_ALPHA1-3 : angle 1.98500 ( 30) hydrogen bonds : bond 0.05444 ( 576) hydrogen bonds : angle 6.10280 ( 1557) SS BOND : bond 0.01199 ( 42) SS BOND : angle 1.50241 ( 84) covalent geometry : bond 0.00604 (20315) covalent geometry : angle 0.87115 (27628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7770 (m-30) cc_final: 0.7406 (m-30) REVERT: A 165 ILE cc_start: 0.7982 (mm) cc_final: 0.7775 (mm) REVERT: B 652 GLN cc_start: 0.7279 (tm-30) cc_final: 0.6940 (tm-30) REVERT: D 266 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8968 (m) REVERT: F 47 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6569 (mt-10) REVERT: F 91 GLU cc_start: 0.7043 (tp30) cc_final: 0.6621 (tp30) REVERT: F 95 MET cc_start: 0.8019 (ttp) cc_final: 0.7664 (ttp) REVERT: F 345 VAL cc_start: 0.8632 (t) cc_final: 0.8233 (t) REVERT: G 648 GLU cc_start: 0.7633 (pt0) cc_final: 0.7360 (mm-30) REVERT: H 80 TYR cc_start: 0.7143 (m-80) cc_final: 0.6887 (m-80) REVERT: K 114 GLN cc_start: 0.7287 (tt0) cc_final: 0.6951 (pt0) REVERT: L 610 TRP cc_start: 0.7436 (t-100) cc_final: 0.6508 (t-100) REVERT: L 648 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6946 (mm-30) REVERT: M 80 TYR cc_start: 0.7115 (m-80) cc_final: 0.6888 (m-80) outliers start: 78 outliers final: 61 residues processed: 371 average time/residue: 0.3210 time to fit residues: 183.2549 Evaluate side-chains 341 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 268 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 443 ILE Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 534 SER Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 77 ASN Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 175 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 195 ASN H 77 ASN L 591 GLN M 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.193328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167661 restraints weight = 29821.644| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.59 r_work: 0.3889 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20421 Z= 0.188 Angle : 0.793 12.562 27904 Z= 0.396 Chirality : 0.048 0.211 3306 Planarity : 0.005 0.064 3430 Dihedral : 9.955 78.255 3905 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.63 % Favored : 94.04 % Rotamer: Outliers : 4.31 % Allowed : 14.29 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2433 helix: -1.27 (0.25), residues: 417 sheet: -0.16 (0.22), residues: 525 loop : -1.68 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 96 HIS 0.004 0.001 HIS A 287 PHE 0.015 0.002 PHE K 391 TYR 0.032 0.002 TYR C 111 ARG 0.009 0.001 ARG F 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 12) link_NAG-ASN : angle 1.85356 ( 36) link_ALPHA1-6 : bond 0.00324 ( 7) link_ALPHA1-6 : angle 1.52779 ( 21) link_BETA1-4 : bond 0.00481 ( 22) link_BETA1-4 : angle 3.09176 ( 66) link_ALPHA1-2 : bond 0.00610 ( 13) link_ALPHA1-2 : angle 1.63433 ( 39) link_ALPHA1-3 : bond 0.01032 ( 10) link_ALPHA1-3 : angle 1.99915 ( 30) hydrogen bonds : bond 0.04582 ( 576) hydrogen bonds : angle 5.79176 ( 1557) SS BOND : bond 0.00437 ( 42) SS BOND : angle 2.49674 ( 84) covalent geometry : bond 0.00438 (20315) covalent geometry : angle 0.76071 (27628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 297 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7818 (m-30) cc_final: 0.7426 (m-30) REVERT: A 207 LYS cc_start: 0.7839 (tptt) cc_final: 0.7445 (tptt) REVERT: B 610 TRP cc_start: 0.7115 (t-100) cc_final: 0.6407 (t-100) REVERT: B 652 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6929 (tm-30) REVERT: D 266 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8956 (m) REVERT: F 47 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6487 (mt-10) REVERT: F 95 MET cc_start: 0.8010 (ttp) cc_final: 0.7670 (ttp) REVERT: F 231 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: F 345 VAL cc_start: 0.8557 (t) cc_final: 0.8189 (t) REVERT: G 540 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: G 648 GLU cc_start: 0.7620 (pt0) cc_final: 0.7307 (mm-30) REVERT: H 80 TYR cc_start: 0.7118 (m-80) cc_final: 0.6853 (m-80) REVERT: I 298 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7378 (tttp) REVERT: L 610 TRP cc_start: 0.7417 (t-100) cc_final: 0.6622 (t-100) REVERT: L 648 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7099 (mm-30) REVERT: L 652 GLN cc_start: 0.7260 (tm-30) cc_final: 0.7040 (tm-30) REVERT: M 80 TYR cc_start: 0.7065 (m-80) cc_final: 0.6730 (m-80) outliers start: 92 outliers final: 61 residues processed: 365 average time/residue: 0.2945 time to fit residues: 165.1861 Evaluate side-chains 335 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 188 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 209 optimal weight: 0.0050 chunk 169 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN F 114 GLN K 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.198186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173133 restraints weight = 30021.086| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.40 r_work: 0.3948 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20421 Z= 0.119 Angle : 0.684 11.046 27904 Z= 0.340 Chirality : 0.045 0.200 3306 Planarity : 0.004 0.045 3430 Dihedral : 8.720 70.843 3905 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.97 % Favored : 94.78 % Rotamer: Outliers : 3.37 % Allowed : 16.16 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2433 helix: -0.92 (0.25), residues: 415 sheet: -0.06 (0.22), residues: 558 loop : -1.46 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 96 HIS 0.003 0.001 HIS K 374 PHE 0.009 0.001 PHE A 391 TYR 0.011 0.001 TYR M 111 ARG 0.006 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 12) link_NAG-ASN : angle 1.47630 ( 36) link_ALPHA1-6 : bond 0.00528 ( 7) link_ALPHA1-6 : angle 1.41654 ( 21) link_BETA1-4 : bond 0.00437 ( 22) link_BETA1-4 : angle 2.75326 ( 66) link_ALPHA1-2 : bond 0.00629 ( 13) link_ALPHA1-2 : angle 1.65014 ( 39) link_ALPHA1-3 : bond 0.01257 ( 10) link_ALPHA1-3 : angle 1.93808 ( 30) hydrogen bonds : bond 0.03833 ( 576) hydrogen bonds : angle 5.42595 ( 1557) SS BOND : bond 0.00274 ( 42) SS BOND : angle 1.47732 ( 84) covalent geometry : bond 0.00254 (20315) covalent geometry : angle 0.65986 (27628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 2.244 Fit side-chains REVERT: A 107 ASP cc_start: 0.7859 (m-30) cc_final: 0.7538 (m-30) REVERT: A 207 LYS cc_start: 0.7675 (tptt) cc_final: 0.7385 (tptt) REVERT: B 610 TRP cc_start: 0.7017 (t-100) cc_final: 0.6458 (t-100) REVERT: B 650 GLN cc_start: 0.7928 (tp40) cc_final: 0.7661 (tm-30) REVERT: B 652 GLN cc_start: 0.6938 (tm-30) cc_final: 0.6588 (tm-30) REVERT: D 298 LYS cc_start: 0.7766 (ttpp) cc_final: 0.6847 (tttt) REVERT: D 305 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7521 (tt) REVERT: F 95 MET cc_start: 0.7980 (ttp) cc_final: 0.7690 (ttp) REVERT: F 345 VAL cc_start: 0.8412 (t) cc_final: 0.8085 (t) REVERT: G 648 GLU cc_start: 0.7544 (pt0) cc_final: 0.7276 (mm-30) REVERT: H 80 TYR cc_start: 0.6853 (m-80) cc_final: 0.6611 (m-80) REVERT: I 298 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7354 (tttp) REVERT: L 530 MET cc_start: 0.8600 (mmm) cc_final: 0.8196 (mmm) REVERT: L 610 TRP cc_start: 0.7353 (t-100) cc_final: 0.6657 (t-100) REVERT: L 648 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7068 (mm-30) REVERT: M 80 TYR cc_start: 0.7062 (m-80) cc_final: 0.6648 (m-80) outliers start: 72 outliers final: 40 residues processed: 357 average time/residue: 0.3043 time to fit residues: 167.9237 Evaluate side-chains 315 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 121 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN C 77 ASN F 262 ASN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.167914 restraints weight = 29743.687| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.52 r_work: 0.3894 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20421 Z= 0.172 Angle : 0.745 10.964 27904 Z= 0.369 Chirality : 0.046 0.217 3306 Planarity : 0.004 0.046 3430 Dihedral : 8.847 74.781 3905 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 3.79 % Allowed : 16.53 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2433 helix: -0.88 (0.25), residues: 417 sheet: -0.04 (0.22), residues: 570 loop : -1.46 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 96 HIS 0.003 0.001 HIS A 287 PHE 0.012 0.002 PHE D 319 TYR 0.031 0.002 TYR C 111 ARG 0.008 0.000 ARG H 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 12) link_NAG-ASN : angle 1.63765 ( 36) link_ALPHA1-6 : bond 0.00287 ( 7) link_ALPHA1-6 : angle 1.59298 ( 21) link_BETA1-4 : bond 0.00475 ( 22) link_BETA1-4 : angle 2.71937 ( 66) link_ALPHA1-2 : bond 0.00671 ( 13) link_ALPHA1-2 : angle 1.61269 ( 39) link_ALPHA1-3 : bond 0.01057 ( 10) link_ALPHA1-3 : angle 1.97652 ( 30) hydrogen bonds : bond 0.04089 ( 576) hydrogen bonds : angle 5.43848 ( 1557) SS BOND : bond 0.00442 ( 42) SS BOND : angle 1.79695 ( 84) covalent geometry : bond 0.00401 (20315) covalent geometry : angle 0.72109 (27628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6954 (pp20) REVERT: A 107 ASP cc_start: 0.8015 (m-30) cc_final: 0.7700 (m-30) REVERT: A 433 CYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4732 (t) REVERT: B 610 TRP cc_start: 0.7093 (t-100) cc_final: 0.6549 (t-100) REVERT: B 648 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 650 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7629 (tm-30) REVERT: B 652 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6746 (tm-30) REVERT: D 266 SER cc_start: 0.9145 (t) cc_final: 0.8937 (m) REVERT: D 305 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7333 (tt) REVERT: F 95 MET cc_start: 0.7972 (ttp) cc_final: 0.7668 (ttp) REVERT: F 345 VAL cc_start: 0.8509 (t) cc_final: 0.8169 (t) REVERT: G 540 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: G 648 GLU cc_start: 0.7573 (pt0) cc_final: 0.7170 (mm-30) REVERT: H 80 TYR cc_start: 0.7151 (m-80) cc_final: 0.6939 (m-80) REVERT: L 610 TRP cc_start: 0.7426 (t-100) cc_final: 0.6758 (t-100) REVERT: L 648 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6935 (mm-30) REVERT: M 80 TYR cc_start: 0.7092 (m-80) cc_final: 0.6780 (m-80) outliers start: 81 outliers final: 64 residues processed: 346 average time/residue: 0.3121 time to fit residues: 166.9498 Evaluate side-chains 335 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 389 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 539 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165646 restraints weight = 29693.815| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.49 r_work: 0.3867 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20421 Z= 0.206 Angle : 0.779 12.507 27904 Z= 0.387 Chirality : 0.047 0.185 3306 Planarity : 0.004 0.046 3430 Dihedral : 9.110 78.021 3905 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.29 % Favored : 93.42 % Rotamer: Outliers : 4.31 % Allowed : 16.77 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2433 helix: -0.84 (0.26), residues: 389 sheet: -0.12 (0.22), residues: 574 loop : -1.45 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 96 HIS 0.004 0.001 HIS A 287 PHE 0.013 0.002 PHE D 319 TYR 0.038 0.002 TYR C 111 ARG 0.005 0.000 ARG M 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 12) link_NAG-ASN : angle 1.71080 ( 36) link_ALPHA1-6 : bond 0.00214 ( 7) link_ALPHA1-6 : angle 1.70039 ( 21) link_BETA1-4 : bond 0.00462 ( 22) link_BETA1-4 : angle 2.69445 ( 66) link_ALPHA1-2 : bond 0.00787 ( 13) link_ALPHA1-2 : angle 1.61938 ( 39) link_ALPHA1-3 : bond 0.00966 ( 10) link_ALPHA1-3 : angle 1.95843 ( 30) hydrogen bonds : bond 0.04323 ( 576) hydrogen bonds : angle 5.54422 ( 1557) SS BOND : bond 0.00441 ( 42) SS BOND : angle 2.15751 ( 84) covalent geometry : bond 0.00484 (20315) covalent geometry : angle 0.75353 (27628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 283 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8047 (m-30) cc_final: 0.7741 (m-30) REVERT: A 114 GLN cc_start: 0.7732 (tt0) cc_final: 0.6958 (tt0) REVERT: A 165 ILE cc_start: 0.8069 (mm) cc_final: 0.7682 (mt) REVERT: B 610 TRP cc_start: 0.7121 (t-100) cc_final: 0.6742 (t-100) REVERT: B 648 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7290 (mm-30) REVERT: B 652 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6814 (tm-30) REVERT: D 282 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7308 (mm-30) REVERT: D 305 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7332 (tt) REVERT: F 95 MET cc_start: 0.7876 (ttp) cc_final: 0.7588 (ttp) REVERT: F 345 VAL cc_start: 0.8545 (t) cc_final: 0.8220 (t) REVERT: G 540 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: G 648 GLU cc_start: 0.7514 (pt0) cc_final: 0.7147 (mm-30) REVERT: K 107 ASP cc_start: 0.7871 (m-30) cc_final: 0.7520 (m-30) REVERT: L 610 TRP cc_start: 0.7231 (t-100) cc_final: 0.6536 (t-100) REVERT: L 648 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6960 (mm-30) REVERT: M 80 TYR cc_start: 0.7223 (m-80) cc_final: 0.6930 (m-80) REVERT: M 115 ASP cc_start: 0.7518 (t0) cc_final: 0.7250 (t0) outliers start: 92 outliers final: 74 residues processed: 348 average time/residue: 0.3012 time to fit residues: 161.3271 Evaluate side-chains 345 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 269 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 389 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 443 ILE Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 83 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.187039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.162364 restraints weight = 29877.761| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.44 r_work: 0.3830 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20421 Z= 0.258 Angle : 0.847 17.423 27904 Z= 0.417 Chirality : 0.050 0.207 3306 Planarity : 0.005 0.047 3430 Dihedral : 9.491 80.213 3905 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.23 % Favored : 92.40 % Rotamer: Outliers : 4.36 % Allowed : 17.89 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2433 helix: -1.34 (0.24), residues: 426 sheet: -0.34 (0.21), residues: 585 loop : -1.65 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP K 96 HIS 0.005 0.001 HIS A 287 PHE 0.016 0.002 PHE D 319 TYR 0.044 0.002 TYR M 111 ARG 0.011 0.001 ARG H 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 12) link_NAG-ASN : angle 1.82751 ( 36) link_ALPHA1-6 : bond 0.00213 ( 7) link_ALPHA1-6 : angle 1.86221 ( 21) link_BETA1-4 : bond 0.00472 ( 22) link_BETA1-4 : angle 2.75220 ( 66) link_ALPHA1-2 : bond 0.00792 ( 13) link_ALPHA1-2 : angle 1.63686 ( 39) link_ALPHA1-3 : bond 0.00834 ( 10) link_ALPHA1-3 : angle 1.96770 ( 30) hydrogen bonds : bond 0.04575 ( 576) hydrogen bonds : angle 5.74428 ( 1557) SS BOND : bond 0.00529 ( 42) SS BOND : angle 2.33945 ( 84) covalent geometry : bond 0.00612 (20315) covalent geometry : angle 0.82187 (27628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 287 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8356 (tp30) cc_final: 0.8134 (tp30) REVERT: A 107 ASP cc_start: 0.8078 (m-30) cc_final: 0.7756 (m-30) REVERT: A 165 ILE cc_start: 0.8105 (mm) cc_final: 0.7742 (mt) REVERT: B 573 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (mt) REVERT: B 610 TRP cc_start: 0.7178 (t-100) cc_final: 0.6846 (t-100) REVERT: B 648 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7190 (mm-30) REVERT: B 652 GLN cc_start: 0.7413 (tm-30) cc_final: 0.7023 (tm-30) REVERT: D 305 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7516 (tt) REVERT: F 95 MET cc_start: 0.7892 (ttp) cc_final: 0.7619 (ttp) REVERT: F 345 VAL cc_start: 0.8563 (t) cc_final: 0.8198 (t) REVERT: G 540 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: G 648 GLU cc_start: 0.7558 (pt0) cc_final: 0.7255 (mm-30) REVERT: H 80 TYR cc_start: 0.7348 (m-80) cc_final: 0.7117 (m-80) REVERT: L 610 TRP cc_start: 0.7422 (t-100) cc_final: 0.6798 (t-100) REVERT: L 648 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6978 (mm-30) REVERT: M 80 TYR cc_start: 0.7332 (m-80) cc_final: 0.7059 (m-80) outliers start: 93 outliers final: 77 residues processed: 354 average time/residue: 0.3023 time to fit residues: 164.3939 Evaluate side-chains 354 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 274 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 389 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 539 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 234 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 262 ASN A 425 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.190807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.165892 restraints weight = 29629.031| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.57 r_work: 0.3875 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20421 Z= 0.153 Angle : 0.726 10.967 27904 Z= 0.359 Chirality : 0.046 0.185 3306 Planarity : 0.004 0.046 3430 Dihedral : 8.777 75.229 3905 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.55 % Favored : 94.12 % Rotamer: Outliers : 3.47 % Allowed : 18.41 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2433 helix: -0.79 (0.26), residues: 402 sheet: -0.21 (0.22), residues: 577 loop : -1.50 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP K 96 HIS 0.003 0.001 HIS F 105 PHE 0.009 0.001 PHE I 294 TYR 0.024 0.002 TYR M 111 ARG 0.005 0.000 ARG H 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 12) link_NAG-ASN : angle 1.59919 ( 36) link_ALPHA1-6 : bond 0.00272 ( 7) link_ALPHA1-6 : angle 1.66441 ( 21) link_BETA1-4 : bond 0.00382 ( 22) link_BETA1-4 : angle 2.56446 ( 66) link_ALPHA1-2 : bond 0.00636 ( 13) link_ALPHA1-2 : angle 1.57146 ( 39) link_ALPHA1-3 : bond 0.00901 ( 10) link_ALPHA1-3 : angle 1.79078 ( 30) hydrogen bonds : bond 0.03948 ( 576) hydrogen bonds : angle 5.41553 ( 1557) SS BOND : bond 0.00409 ( 42) SS BOND : angle 1.65192 ( 84) covalent geometry : bond 0.00354 (20315) covalent geometry : angle 0.70392 (27628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8099 (m-30) cc_final: 0.7775 (m-30) REVERT: A 165 ILE cc_start: 0.8061 (mm) cc_final: 0.7727 (mt) REVERT: B 573 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 610 TRP cc_start: 0.7084 (t-100) cc_final: 0.6260 (t-100) REVERT: B 648 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 650 GLN cc_start: 0.8089 (tp40) cc_final: 0.7812 (tm-30) REVERT: B 652 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6893 (tm-30) REVERT: D 305 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7382 (tt) REVERT: F 95 MET cc_start: 0.7833 (ttp) cc_final: 0.7597 (ttp) REVERT: F 345 VAL cc_start: 0.8514 (t) cc_final: 0.8193 (t) REVERT: G 540 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: G 648 GLU cc_start: 0.7570 (pt0) cc_final: 0.7197 (mm-30) REVERT: H 80 TYR cc_start: 0.7284 (m-80) cc_final: 0.6970 (m-80) REVERT: L 610 TRP cc_start: 0.7368 (t-100) cc_final: 0.6789 (t-100) REVERT: L 648 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6994 (mm-30) REVERT: M 80 TYR cc_start: 0.7280 (m-80) cc_final: 0.6956 (m-80) REVERT: M 84 ARG cc_start: 0.7019 (mpp80) cc_final: 0.6488 (mpt180) outliers start: 74 outliers final: 58 residues processed: 344 average time/residue: 0.3320 time to fit residues: 175.7306 Evaluate side-chains 337 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 258 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 389 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 443 ILE Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 179 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN H 77 ASN ** L 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166841 restraints weight = 29723.442| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.57 r_work: 0.3884 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20421 Z= 0.143 Angle : 0.708 10.214 27904 Z= 0.351 Chirality : 0.045 0.191 3306 Planarity : 0.004 0.046 3430 Dihedral : 8.378 74.210 3905 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.25 % Favored : 93.51 % Rotamer: Outliers : 3.09 % Allowed : 19.20 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2433 helix: -0.64 (0.26), residues: 402 sheet: -0.19 (0.22), residues: 591 loop : -1.42 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP K 96 HIS 0.004 0.001 HIS A 105 PHE 0.009 0.001 PHE D 319 TYR 0.023 0.001 TYR C 111 ARG 0.003 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 12) link_NAG-ASN : angle 1.45635 ( 36) link_ALPHA1-6 : bond 0.00352 ( 7) link_ALPHA1-6 : angle 1.57912 ( 21) link_BETA1-4 : bond 0.00406 ( 22) link_BETA1-4 : angle 2.48364 ( 66) link_ALPHA1-2 : bond 0.00603 ( 13) link_ALPHA1-2 : angle 1.57385 ( 39) link_ALPHA1-3 : bond 0.00868 ( 10) link_ALPHA1-3 : angle 1.76151 ( 30) hydrogen bonds : bond 0.03774 ( 576) hydrogen bonds : angle 5.23039 ( 1557) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.50296 ( 84) covalent geometry : bond 0.00330 (20315) covalent geometry : angle 0.68801 (27628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8396 (tp30) cc_final: 0.8171 (tp30) REVERT: A 107 ASP cc_start: 0.8102 (m-30) cc_final: 0.7752 (m-30) REVERT: A 165 ILE cc_start: 0.8064 (mm) cc_final: 0.7733 (mt) REVERT: B 544 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5637 (tp) REVERT: B 573 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (mt) REVERT: B 610 TRP cc_start: 0.7065 (t-100) cc_final: 0.6301 (t-100) REVERT: B 648 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 650 GLN cc_start: 0.8064 (tp40) cc_final: 0.7816 (tm-30) REVERT: B 652 GLN cc_start: 0.7334 (tm-30) cc_final: 0.6973 (tm-30) REVERT: D 305 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7367 (tt) REVERT: F 95 MET cc_start: 0.7789 (ttp) cc_final: 0.7576 (ttp) REVERT: F 107 ASP cc_start: 0.8221 (m-30) cc_final: 0.7897 (m-30) REVERT: F 345 VAL cc_start: 0.8491 (t) cc_final: 0.8179 (t) REVERT: G 540 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: G 648 GLU cc_start: 0.7493 (pt0) cc_final: 0.7073 (mm-30) REVERT: H 80 TYR cc_start: 0.7227 (m-80) cc_final: 0.6909 (m-80) REVERT: I 335 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7157 (t) REVERT: K 107 ASP cc_start: 0.7880 (m-30) cc_final: 0.7535 (m-30) REVERT: L 610 TRP cc_start: 0.7281 (t-100) cc_final: 0.6760 (t-100) REVERT: L 648 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7202 (mm-30) REVERT: M 80 TYR cc_start: 0.7241 (m-80) cc_final: 0.6850 (m-80) REVERT: M 84 ARG cc_start: 0.7043 (mpp80) cc_final: 0.6507 (mpt180) REVERT: N 234 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5576 (tt) outliers start: 66 outliers final: 54 residues processed: 331 average time/residue: 0.3076 time to fit residues: 156.3035 Evaluate side-chains 343 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 258 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 539 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 102 optimal weight: 0.0050 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 236 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.190379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165458 restraints weight = 29807.394| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.54 r_work: 0.3864 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20421 Z= 0.173 Angle : 0.732 11.352 27904 Z= 0.363 Chirality : 0.046 0.193 3306 Planarity : 0.004 0.047 3430 Dihedral : 8.538 75.089 3905 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.25 % Favored : 93.46 % Rotamer: Outliers : 3.37 % Allowed : 19.34 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2433 helix: -0.64 (0.27), residues: 402 sheet: -0.21 (0.22), residues: 591 loop : -1.44 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP K 96 HIS 0.004 0.001 HIS A 105 PHE 0.011 0.002 PHE D 319 TYR 0.030 0.002 TYR M 111 ARG 0.003 0.000 ARG M 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 12) link_NAG-ASN : angle 1.54877 ( 36) link_ALPHA1-6 : bond 0.00253 ( 7) link_ALPHA1-6 : angle 1.68865 ( 21) link_BETA1-4 : bond 0.00407 ( 22) link_BETA1-4 : angle 2.48976 ( 66) link_ALPHA1-2 : bond 0.00592 ( 13) link_ALPHA1-2 : angle 1.56636 ( 39) link_ALPHA1-3 : bond 0.00823 ( 10) link_ALPHA1-3 : angle 1.78460 ( 30) hydrogen bonds : bond 0.03912 ( 576) hydrogen bonds : angle 5.29479 ( 1557) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.70678 ( 84) covalent geometry : bond 0.00407 (20315) covalent geometry : angle 0.71121 (27628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8792.03 seconds wall clock time: 153 minutes 26.22 seconds (9206.22 seconds total)