Starting phenix.real_space_refine on Tue Oct 15 04:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8say_40284/10_2024/8say_40284_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8say_40284/10_2024/8say_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8say_40284/10_2024/8say_40284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8say_40284/10_2024/8say_40284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8say_40284/10_2024/8say_40284_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8say_40284/10_2024/8say_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 11.61, per 1000 atoms: 0.58 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: 5.78 Conformation dependent library (CDL) restraints added in 2.3 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: 2.75 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: 7.60 Time building geometry restraints manager: 6.54 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 45.710 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.290 ------------------------------------------------------------------------------- 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 20315 Z= 0.393 Angle : 1.027 13.650 27628 Z= 0.520 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 2.325 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: 0.3429 time to fit residues: 284.0251 Evaluate side-chains 324 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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: 9.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 20315 Z= 0.237 Angle : 0.782 10.390 27628 Z= 0.398 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 *********************** 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 fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6989 (tptt) REVERT: B 530 MET cc_start: 0.7267 (mmm) cc_final: 0.6688 (mmm) REVERT: B 589 ASP cc_start: 0.8227 (m-30) cc_final: 0.7927 (m-30) REVERT: B 652 GLN cc_start: 0.6874 (tm-30) cc_final: 0.6585 (tm-30) REVERT: D 298 LYS cc_start: 0.7742 (ttpp) cc_final: 0.6977 (tttt) REVERT: F 95 MET cc_start: 0.7927 (ttp) cc_final: 0.7645 (ttp) REVERT: F 108 ILE cc_start: 0.8120 (tt) cc_final: 0.7898 (tt) REVERT: F 345 VAL cc_start: 0.8506 (t) cc_final: 0.8172 (t) REVERT: G 540 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: G 614 TRP cc_start: 0.4547 (m-10) cc_final: 0.3878 (m-10) REVERT: G 622 ILE cc_start: 0.6670 (mm) cc_final: 0.6414 (pt) REVERT: I 298 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7338 (tttp) REVERT: K 69 TRP cc_start: 0.4187 (p-90) cc_final: 0.3533 (p-90) REVERT: L 540 GLN cc_start: 0.8067 (mt0) cc_final: 0.7768 (mt0) REVERT: L 610 TRP cc_start: 0.7515 (t-100) cc_final: 0.6692 (t-100) REVERT: M 58 THR cc_start: 0.8955 (m) cc_final: 0.8687 (t) REVERT: N 298 LYS cc_start: 0.7753 (ttpp) cc_final: 0.6974 (ttmm) outliers start: 50 outliers final: 34 residues processed: 383 average time/residue: 0.3394 time to fit residues: 195.2388 Evaluate side-chains 317 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 122 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 221 optimal weight: 0.4980 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS F 195 ASN G 540 GLN G 590 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20315 Z= 0.186 Angle : 0.717 10.404 27628 Z= 0.363 Chirality : 0.046 0.194 3306 Planarity : 0.004 0.050 3430 Dihedral : 10.422 77.695 3905 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 2.58 % Allowed : 12.65 % Favored : 84.78 % 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 (0.16), residues: 2433 helix: -0.93 (0.26), residues: 384 sheet: -0.00 (0.22), residues: 503 loop : -1.49 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 623 HIS 0.002 0.001 HIS F 105 PHE 0.014 0.001 PHE A 391 TYR 0.020 0.001 TYR H 111 ARG 0.008 0.000 ARG F 166 *********************** 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 380 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 325 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7491 (m-30) cc_final: 0.7174 (m-30) REVERT: B 610 TRP cc_start: 0.6626 (t-100) cc_final: 0.6049 (t-100) REVERT: B 652 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6636 (tm-30) REVERT: D 298 LYS cc_start: 0.7766 (ttpp) cc_final: 0.7033 (tttt) REVERT: F 91 GLU cc_start: 0.6790 (tp30) cc_final: 0.6403 (tp30) REVERT: F 95 MET cc_start: 0.7856 (ttp) cc_final: 0.7522 (ttp) REVERT: F 108 ILE cc_start: 0.8100 (tt) cc_final: 0.7854 (tt) REVERT: F 345 VAL cc_start: 0.8403 (t) cc_final: 0.8049 (t) REVERT: G 602 LEU cc_start: 0.6361 (pt) cc_final: 0.6057 (pt) REVERT: G 614 TRP cc_start: 0.4623 (m-10) cc_final: 0.4033 (m-10) REVERT: G 626 MET cc_start: 0.4870 (ttm) cc_final: 0.4538 (ttm) REVERT: I 298 LYS cc_start: 0.7742 (ttpp) cc_final: 0.7298 (tttp) REVERT: L 610 TRP cc_start: 0.7362 (t-100) cc_final: 0.6747 (t-100) REVERT: L 648 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6924 (mm-30) REVERT: N 298 LYS cc_start: 0.7719 (ttpp) cc_final: 0.6993 (ttmm) outliers start: 55 outliers final: 35 residues processed: 361 average time/residue: 0.3276 time to fit residues: 181.0152 Evaluate side-chains 317 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 LEU 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 69 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 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 161 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 322 SER 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 271 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 328 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 H 77 ASN K 72 HIS L 591 GLN L 650 GLN N 301 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20315 Z= 0.319 Angle : 0.783 12.942 27628 Z= 0.395 Chirality : 0.049 0.264 3306 Planarity : 0.005 0.052 3430 Dihedral : 9.812 78.799 3905 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.33 % Favored : 93.38 % Rotamer: Outliers : 4.12 % Allowed : 13.96 % Favored : 81.92 % 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: -1.68 (0.16), residues: 2433 helix: -1.05 (0.25), residues: 398 sheet: -0.07 (0.22), residues: 525 loop : -1.58 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 96 HIS 0.005 0.001 HIS A 287 PHE 0.015 0.002 PHE N 331 TYR 0.042 0.002 TYR C 111 ARG 0.009 0.001 ARG H 62 *********************** 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 388 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 300 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7528 (m-30) cc_final: 0.7248 (m-30) REVERT: A 207 LYS cc_start: 0.7322 (tptt) cc_final: 0.7031 (tptt) REVERT: B 610 TRP cc_start: 0.6951 (t-100) cc_final: 0.6203 (t-100) REVERT: B 652 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6793 (tm-30) REVERT: D 266 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.9112 (m) REVERT: F 95 MET cc_start: 0.7964 (ttp) cc_final: 0.7624 (ttp) REVERT: F 345 VAL cc_start: 0.8498 (t) cc_final: 0.8109 (t) REVERT: L 610 TRP cc_start: 0.7390 (t-100) cc_final: 0.6691 (t-100) REVERT: L 648 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7051 (mm-30) REVERT: M 80 TYR cc_start: 0.7112 (m-80) cc_final: 0.6871 (m-80) outliers start: 88 outliers final: 55 residues processed: 362 average time/residue: 0.3551 time to fit residues: 199.9318 Evaluate side-chains 318 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 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 C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 81 MET 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 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 443 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain I residue 299 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 189 SER Chi-restraints excluded: chain K residue 198 THR 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 364 SER Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 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 195 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 59 optimal weight: 0.0030 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 650 GLN B 658 GLN C 77 ASN H 77 ASN M 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20315 Z= 0.284 Angle : 0.751 12.407 27628 Z= 0.378 Chirality : 0.047 0.243 3306 Planarity : 0.004 0.074 3430 Dihedral : 9.389 77.262 3905 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.17 % Favored : 93.55 % Rotamer: Outliers : 4.07 % Allowed : 15.55 % Favored : 80.37 % 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: -1.64 (0.16), residues: 2433 helix: -1.08 (0.25), residues: 418 sheet: -0.04 (0.23), residues: 512 loop : -1.52 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 96 HIS 0.004 0.001 HIS A 287 PHE 0.014 0.002 PHE A 376 TYR 0.031 0.002 TYR C 111 ARG 0.010 0.001 ARG A 166 *********************** 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 370 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 283 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7454 (m-30) cc_final: 0.7185 (m-30) REVERT: A 207 LYS cc_start: 0.7306 (tptt) cc_final: 0.6941 (tptt) REVERT: B 610 TRP cc_start: 0.6960 (t-100) cc_final: 0.6401 (t-100) REVERT: B 650 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7701 (tm-30) REVERT: B 652 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6902 (tm-30) REVERT: F 95 MET cc_start: 0.7972 (ttp) cc_final: 0.7643 (ttp) REVERT: F 345 VAL cc_start: 0.8453 (t) cc_final: 0.8084 (t) REVERT: L 610 TRP cc_start: 0.7400 (t-100) cc_final: 0.6695 (t-100) REVERT: L 648 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7110 (mm-30) outliers start: 87 outliers final: 64 residues processed: 345 average time/residue: 0.3127 time to fit residues: 165.4002 Evaluate side-chains 325 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 261 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain A residue 120 VAL 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 265 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 ASP 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 69 THR Chi-restraints excluded: chain C residue 77 ASN 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 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 189 SER Chi-restraints excluded: chain F residue 198 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 G residue 534 SER 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 253 THR Chi-restraints excluded: chain I residue 299 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 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 364 SER Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 534 SER Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 77 ASN Chi-restraints excluded: chain M residue 121 THR 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 79 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN H 77 ASN L 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 20315 Z= 0.539 Angle : 0.964 18.670 27628 Z= 0.484 Chirality : 0.054 0.319 3306 Planarity : 0.006 0.082 3430 Dihedral : 10.424 86.170 3905 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.44 % Favored : 92.19 % Rotamer: Outliers : 5.06 % Allowed : 15.69 % Favored : 79.25 % 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: -2.20 (0.16), residues: 2433 helix: -1.51 (0.24), residues: 409 sheet: -0.36 (0.22), residues: 543 loop : -1.95 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 96 HIS 0.007 0.002 HIS A 287 PHE 0.023 0.003 PHE H 114 TYR 0.067 0.003 TYR C 111 ARG 0.009 0.001 ARG H 62 *********************** 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 400 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 292 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8004 (tp30) cc_final: 0.7790 (tp30) REVERT: B 610 TRP cc_start: 0.7202 (t-100) cc_final: 0.6829 (t-100) REVERT: B 648 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7114 (mm-30) REVERT: B 652 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7091 (tm-30) REVERT: L 610 TRP cc_start: 0.7368 (t-100) cc_final: 0.6770 (t-100) REVERT: L 648 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7071 (mm-30) REVERT: M 80 TYR cc_start: 0.7316 (m-80) cc_final: 0.7039 (m-80) outliers start: 108 outliers final: 90 residues processed: 369 average time/residue: 0.3352 time to fit residues: 188.2231 Evaluate side-chains 350 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 260 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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 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 209 THR Chi-restraints excluded: chain A residue 213 ILE 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 340 ASP 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 B residue 534 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 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 C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL 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 314 ASP 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 189 SER Chi-restraints excluded: chain F residue 198 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 F residue 443 ILE Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 539 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 H residue 121 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 335 THR 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 218 CYS 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 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 534 SER Chi-restraints excluded: chain L residue 545 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 L residue 661 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 314 ASP 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 226 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 171 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN K 105 HIS ** L 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 650 GLN ** L 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN N 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20315 Z= 0.192 Angle : 0.703 10.362 27628 Z= 0.355 Chirality : 0.046 0.215 3306 Planarity : 0.004 0.045 3430 Dihedral : 8.953 73.654 3905 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.64 % Favored : 95.03 % Rotamer: Outliers : 3.28 % Allowed : 18.50 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.67 (0.16), residues: 2433 helix: -0.90 (0.26), residues: 407 sheet: -0.23 (0.21), residues: 583 loop : -1.59 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 96 HIS 0.004 0.001 HIS A 105 PHE 0.009 0.001 PHE K 382 TYR 0.014 0.001 TYR I 318 ARG 0.012 0.001 ARG A 166 *********************** 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 360 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 610 TRP cc_start: 0.7077 (t-100) cc_final: 0.6502 (t-100) REVERT: B 621 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5094 (pt0) REVERT: B 648 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7190 (mm-30) REVERT: B 652 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6701 (tm-30) REVERT: D 305 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7259 (tt) REVERT: F 95 MET cc_start: 0.7595 (ttp) cc_final: 0.7379 (ttp) REVERT: F 345 VAL cc_start: 0.8419 (t) cc_final: 0.8080 (t) REVERT: G 540 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: G 602 LEU cc_start: 0.6373 (pt) cc_final: 0.5925 (pt) REVERT: L 610 TRP cc_start: 0.7350 (t-100) cc_final: 0.6685 (t-100) REVERT: M 80 TYR cc_start: 0.6998 (m-80) cc_final: 0.6564 (m-80) REVERT: M 115 ASP cc_start: 0.7350 (t0) cc_final: 0.7054 (t0) outliers start: 70 outliers final: 51 residues processed: 334 average time/residue: 0.3294 time to fit residues: 167.1300 Evaluate side-chains 319 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 265 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 340 ASP 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 544 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain F residue 92 ASN 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 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET 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 253 THR 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 217 TYR Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL 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 595 ILE 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 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 93 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 159 optimal weight: 0.0870 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN F 262 ASN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN H 77 ASN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 656 ASN M 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20315 Z= 0.237 Angle : 0.713 10.455 27628 Z= 0.360 Chirality : 0.047 0.274 3306 Planarity : 0.004 0.045 3430 Dihedral : 8.728 73.571 3905 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 3.33 % Allowed : 18.59 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.59 (0.17), residues: 2433 helix: -0.79 (0.26), residues: 407 sheet: -0.20 (0.22), residues: 573 loop : -1.54 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP K 96 HIS 0.004 0.001 HIS A 105 PHE 0.011 0.002 PHE D 319 TYR 0.026 0.002 TYR C 111 ARG 0.008 0.000 ARG A 166 *********************** 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 355 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 284 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8317 (m100) cc_final: 0.8097 (m100) REVERT: B 610 TRP cc_start: 0.7068 (t-100) cc_final: 0.6572 (t-100) REVERT: B 621 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5249 (pt0) REVERT: B 648 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 652 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6705 (tm-30) REVERT: D 305 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7175 (tt) REVERT: F 95 MET cc_start: 0.7516 (ttp) cc_final: 0.7308 (ttp) REVERT: F 345 VAL cc_start: 0.8449 (t) cc_final: 0.8136 (t) REVERT: G 540 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: L 610 TRP cc_start: 0.7396 (t-100) cc_final: 0.6866 (t-100) REVERT: M 80 TYR cc_start: 0.7004 (m-80) cc_final: 0.6681 (m-80) REVERT: M 115 ASP cc_start: 0.7419 (t0) cc_final: 0.7169 (t0) outliers start: 71 outliers final: 56 residues processed: 331 average time/residue: 0.3380 time to fit residues: 169.7917 Evaluate side-chains 330 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 104 MET 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 271 VAL Chi-restraints excluded: chain A residue 340 ASP 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 573 ILE Chi-restraints excluded: chain B residue 621 GLU 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 C residue 121 THR 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 114 GLN 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 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET 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 253 THR 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 115 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 209 THR Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL 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 647 GLU Chi-restraints excluded: chain M residue 51 ILE 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 224 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 656 ASN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20315 Z= 0.385 Angle : 0.807 13.656 27628 Z= 0.406 Chirality : 0.049 0.288 3306 Planarity : 0.005 0.047 3430 Dihedral : 9.348 78.912 3905 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.27 % Favored : 92.40 % Rotamer: Outliers : 3.89 % Allowed : 18.17 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.80 (0.16), residues: 2433 helix: -1.04 (0.25), residues: 421 sheet: -0.27 (0.21), residues: 585 loop : -1.69 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP K 96 HIS 0.005 0.001 HIS A 287 PHE 0.016 0.002 PHE H 114 TYR 0.042 0.002 TYR M 111 ARG 0.012 0.001 ARG H 62 *********************** 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 367 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 284 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 610 TRP cc_start: 0.7090 (t-100) cc_final: 0.6839 (t-100) REVERT: B 621 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5354 (pt0) REVERT: B 648 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7200 (mm-30) REVERT: B 652 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6899 (tm-30) REVERT: G 540 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: L 610 TRP cc_start: 0.7519 (t-100) cc_final: 0.6971 (t-100) REVERT: M 80 TYR cc_start: 0.7138 (m-80) cc_final: 0.6836 (m-80) REVERT: M 84 ARG cc_start: 0.7063 (mpp80) cc_final: 0.6609 (mpt180) outliers start: 83 outliers final: 73 residues processed: 335 average time/residue: 0.3310 time to fit residues: 168.8465 Evaluate side-chains 350 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 275 time to evaluate : 2.386 ------------------------------------------------------------------------------- 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 110 SER 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 198 THR Chi-restraints excluded: chain A residue 213 ILE 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 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 621 GLU 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 C residue 121 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 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 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 198 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET 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 240 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 115 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 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 218 CYS 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 389 ASN Chi-restraints excluded: chain K residue 400 ILE 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 534 SER Chi-restraints excluded: chain L residue 580 VAL 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 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 230 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20315 Z= 0.201 Angle : 0.697 10.169 27628 Z= 0.353 Chirality : 0.046 0.248 3306 Planarity : 0.004 0.045 3430 Dihedral : 8.592 73.408 3905 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 2.95 % Allowed : 19.16 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2433 helix: -0.62 (0.27), residues: 402 sheet: -0.16 (0.22), residues: 581 loop : -1.50 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP K 96 HIS 0.004 0.001 HIS A 105 PHE 0.008 0.001 PHE C 114 TYR 0.025 0.001 TYR C 111 ARG 0.007 0.001 ARG A 166 ********************** 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 352 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 610 TRP cc_start: 0.7058 (t-100) cc_final: 0.6605 (t-100) REVERT: B 621 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5338 (pt0) REVERT: B 648 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7110 (mm-30) REVERT: B 652 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6925 (tm-30) REVERT: D 279 MET cc_start: 0.5963 (mmt) cc_final: 0.5735 (mmm) REVERT: D 305 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7233 (tt) REVERT: F 345 VAL cc_start: 0.8427 (t) cc_final: 0.8079 (t) REVERT: F 475 MET cc_start: 0.6847 (mmt) cc_final: 0.6605 (mmt) REVERT: G 540 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: K 107 ASP cc_start: 0.7496 (m-30) cc_final: 0.7168 (m-30) REVERT: L 610 TRP cc_start: 0.7429 (t-100) cc_final: 0.6925 (t-100) REVERT: M 80 TYR cc_start: 0.7132 (m-80) cc_final: 0.6791 (m-80) REVERT: M 84 ARG cc_start: 0.6902 (mpp80) cc_final: 0.6461 (mpt180) outliers start: 63 outliers final: 52 residues processed: 326 average time/residue: 0.3297 time to fit residues: 163.9524 Evaluate side-chains 332 residues out of total 2135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 277 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 110 SER 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 189 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 ASP 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 573 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 305 LEU 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 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 198 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 602 LEU Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 115 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 209 THR Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL 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 647 GLU 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 205 optimal weight: 0.0170 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 0.0670 chunk 53 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 overall best weight: 4.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN L 543 ASN ** M 52 ASN ** 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 = 0.4291 r_free = 0.4291 target = 0.187581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.162764 restraints weight = 29602.635| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.38 r_work: 0.3857 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 20315 Z= 0.360 Angle : 0.790 13.104 27628 Z= 0.398 Chirality : 0.049 0.281 3306 Planarity : 0.005 0.048 3430 Dihedral : 9.148 77.918 3905 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.40 % Favored : 92.27 % Rotamer: Outliers : 3.65 % Allowed : 18.88 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.66 (0.17), residues: 2433 helix: -0.76 (0.26), residues: 402 sheet: -0.21 (0.22), residues: 587 loop : -1.63 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 96 HIS 0.005 0.001 HIS A 287 PHE 0.015 0.002 PHE D 319 TYR 0.048 0.002 TYR C 111 ARG 0.006 0.001 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4398.26 seconds wall clock time: 81 minutes 12.83 seconds (4872.83 seconds total)