Starting phenix.real_space_refine on Sun Oct 12 01:16:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8say_40284/10_2025/8say_40284_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8say_40284/10_2025/8say_40284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8say_40284/10_2025/8say_40284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8say_40284/10_2025/8say_40284.map" model { file = "/net/cci-nas-00/data/ceres_data/8say_40284/10_2025/8say_40284_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8say_40284/10_2025/8say_40284_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.83, per 1000 atoms: 0.24 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: 2.08 Conformation dependent library (CDL) restraints added in 746.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.66 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: 3.75 Time building geometry restraints manager: 2.67 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20421 Z= 0.287 Angle : 1.084 18.407 27904 Z= 0.532 Chirality : 0.055 0.337 3306 Planarity : 0.006 0.078 3430 Dihedral : 16.665 112.759 8325 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.06 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.019 0.001 ARG C 62 TYR 0.035 0.002 TYR C 111 PHE 0.028 0.002 PHE K 382 TRP 0.024 0.003 TRP C 101 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00608 (20315) covalent geometry : angle 1.02736 (27628) SS BOND : bond 0.00709 ( 42) SS BOND : angle 2.09058 ( 84) hydrogen bonds : bond 0.23463 ( 576) hydrogen bonds : angle 9.13049 ( 1557) link_ALPHA1-2 : bond 0.01304 ( 13) link_ALPHA1-2 : angle 4.15534 ( 39) link_ALPHA1-3 : bond 0.01132 ( 10) link_ALPHA1-3 : angle 4.00407 ( 30) link_ALPHA1-6 : bond 0.01022 ( 7) link_ALPHA1-6 : angle 2.69613 ( 21) link_BETA1-4 : bond 0.00693 ( 22) link_BETA1-4 : angle 5.19336 ( 66) link_NAG-ASN : bond 0.00365 ( 12) link_NAG-ASN : angle 2.33399 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.7861 (tt) cc_final: 0.7608 (tt) REVERT: A 114 GLN cc_start: 0.7162 (tt0) cc_final: 0.6862 (pt0) REVERT: A 434 MET cc_start: 0.7472 (ttp) cc_final: 0.7217 (ttm) REVERT: B 591 GLN cc_start: 0.8168 (tp40) cc_final: 0.7954 (tt0) REVERT: C 91 THR cc_start: 0.8131 (m) cc_final: 0.7828 (t) REVERT: D 298 LYS cc_start: 0.7682 (ttpp) cc_final: 0.6863 (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: 0.7661 (t0) REVERT: F 434 MET cc_start: 0.8335 (ttp) cc_final: 0.8058 (ttm) REVERT: G 610 TRP cc_start: 0.6838 (t-100) cc_final: 0.6622 (m100) REVERT: H 91 THR cc_start: 0.7818 (m) cc_final: 0.7480 (t) REVERT: I 298 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7321 (tttp) REVERT: L 588 ARG cc_start: 0.6869 (ttt-90) cc_final: 0.6604 (ttp80) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.1570 time to fit residues: 131.2469 Evaluate side-chains 325 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 0.0370 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 540 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN C 52 ASN F 105 HIS F 195 ASN F 300 ASN G 540 GLN G 653 GLN H 3 GLN H 6 GLN H 77 ASN K 105 HIS K 300 ASN L 540 GLN L 650 GLN M 65 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.207604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.182189 restraints weight = 30164.135| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.42 r_work: 0.4074 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20421 Z= 0.152 Angle : 0.794 11.681 27904 Z= 0.396 Chirality : 0.049 0.204 3306 Planarity : 0.005 0.060 3430 Dihedral : 11.858 79.037 3905 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 2.34 % Allowed : 9.88 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.16), residues: 2433 helix: -1.01 (0.26), residues: 372 sheet: -0.27 (0.21), residues: 512 loop : -1.56 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 166 TYR 0.019 0.002 TYR H 111 PHE 0.024 0.002 PHE K 391 TRP 0.019 0.002 TRP H 50 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00320 (20315) covalent geometry : angle 0.76572 (27628) SS BOND : bond 0.00808 ( 42) SS BOND : angle 1.11337 ( 84) hydrogen bonds : bond 0.04926 ( 576) hydrogen bonds : angle 6.33580 ( 1557) link_ALPHA1-2 : bond 0.00648 ( 13) link_ALPHA1-2 : angle 1.95598 ( 39) link_ALPHA1-3 : bond 0.01318 ( 10) link_ALPHA1-3 : angle 2.29896 ( 30) link_ALPHA1-6 : bond 0.00465 ( 7) link_ALPHA1-6 : angle 1.44730 ( 21) link_BETA1-4 : bond 0.00587 ( 22) link_BETA1-4 : angle 3.51705 ( 66) link_NAG-ASN : bond 0.00238 ( 12) link_NAG-ASN : angle 1.71143 ( 36) *********************** 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 412 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8085 (tt) cc_final: 0.7862 (tt) REVERT: A 112 TRP cc_start: 0.6875 (t-100) cc_final: 0.6638 (m100) REVERT: A 207 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7343 (tptt) REVERT: B 652 GLN cc_start: 0.6812 (tm-30) cc_final: 0.6465 (tm-30) REVERT: D 298 LYS cc_start: 0.7754 (ttpp) cc_final: 0.6960 (tttt) REVERT: F 95 MET cc_start: 0.7881 (ttp) cc_final: 0.7609 (ttp) REVERT: F 108 ILE cc_start: 0.8108 (tt) cc_final: 0.7893 (tt) REVERT: F 345 VAL cc_start: 0.8461 (t) cc_final: 0.8130 (t) REVERT: G 614 TRP cc_start: 0.4658 (m-10) cc_final: 0.4099 (m-10) REVERT: G 648 GLU cc_start: 0.7371 (pt0) cc_final: 0.7156 (mm-30) REVERT: G 659 ASP cc_start: 0.7792 (m-30) cc_final: 0.7535 (m-30) REVERT: I 298 LYS cc_start: 0.7839 (ttpp) cc_final: 0.7338 (tttp) REVERT: K 69 TRP cc_start: 0.4288 (p-90) cc_final: 0.3614 (p-90) REVERT: K 114 GLN cc_start: 0.6897 (tt0) cc_final: 0.6654 (pt0) REVERT: K 211 GLU cc_start: 0.8050 (pm20) cc_final: 0.7843 (tt0) REVERT: K 348 GLU cc_start: 0.8220 (mp0) cc_final: 0.7814 (mp0) REVERT: L 633 LYS cc_start: 0.7184 (mptt) cc_final: 0.6703 (mptt) REVERT: M 58 THR cc_start: 0.8906 (m) cc_final: 0.8658 (t) REVERT: N 298 LYS cc_start: 0.7534 (ttpp) cc_final: 0.6929 (ttmm) outliers start: 50 outliers final: 30 residues processed: 391 average time/residue: 0.1428 time to fit residues: 85.2262 Evaluate side-chains 322 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 540 GLN 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 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 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 F residue 488 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain K residue 71 THR 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: 9.9990 chunk 16 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 192 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 577 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 77 ASN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 650 GLN L 540 GLN L 650 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN N 301 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.186506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.161482 restraints weight = 29843.599| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.41 r_work: 0.3826 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 20421 Z= 0.404 Angle : 1.114 19.447 27904 Z= 0.549 Chirality : 0.058 0.362 3306 Planarity : 0.007 0.071 3430 Dihedral : 11.928 90.277 3905 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.32 % Favored : 92.19 % Rotamer: Outliers : 4.40 % Allowed : 13.26 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.15), residues: 2433 helix: -1.89 (0.23), residues: 422 sheet: -0.57 (0.21), residues: 514 loop : -2.09 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 98 TYR 0.080 0.004 TYR M 111 PHE 0.028 0.004 PHE H 114 TRP 0.027 0.003 TRP K 112 HIS 0.011 0.002 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00959 (20315) covalent geometry : angle 1.09232 (27628) SS BOND : bond 0.00988 ( 42) SS BOND : angle 1.71476 ( 84) hydrogen bonds : bond 0.06329 ( 576) hydrogen bonds : angle 6.64739 ( 1557) link_ALPHA1-2 : bond 0.01053 ( 13) link_ALPHA1-2 : angle 1.73556 ( 39) link_ALPHA1-3 : bond 0.01070 ( 10) link_ALPHA1-3 : angle 2.21686 ( 30) link_ALPHA1-6 : bond 0.00629 ( 7) link_ALPHA1-6 : angle 1.91687 ( 21) link_BETA1-4 : bond 0.00690 ( 22) link_BETA1-4 : angle 3.60423 ( 66) link_NAG-ASN : bond 0.00862 ( 12) link_NAG-ASN : angle 2.47997 ( 36) *********************** 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 422 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 328 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7913 (m-30) cc_final: 0.7597 (m-30) REVERT: A 114 GLN cc_start: 0.7492 (tt0) cc_final: 0.6868 (tt0) REVERT: A 165 ILE cc_start: 0.8138 (mm) cc_final: 0.7926 (mm) REVERT: A 340 ASP cc_start: 0.7545 (t70) cc_final: 0.7135 (t0) REVERT: A 394 THR cc_start: 0.5640 (OUTLIER) cc_final: 0.5426 (t) REVERT: B 648 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7175 (mm-30) REVERT: B 652 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7092 (tm-30) REVERT: F 91 GLU cc_start: 0.6944 (tp30) cc_final: 0.6620 (tp30) REVERT: F 92 ASN cc_start: 0.7774 (t0) cc_final: 0.7550 (t0) REVERT: F 95 MET cc_start: 0.8039 (ttp) cc_final: 0.7712 (ttp) REVERT: F 340 ASP cc_start: 0.7788 (t70) cc_final: 0.7548 (t0) REVERT: G 648 GLU cc_start: 0.7669 (pt0) cc_final: 0.7408 (mm-30) REVERT: I 266 SER cc_start: 0.9197 (t) cc_final: 0.8988 (m) REVERT: K 340 ASP cc_start: 0.7814 (t70) cc_final: 0.7550 (t0) REVERT: L 610 TRP cc_start: 0.7439 (t-100) cc_final: 0.6621 (t-100) REVERT: L 648 GLU cc_start: 0.7687 (tm-30) cc_final: 0.6813 (mm-30) REVERT: L 650 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7882 (tm-30) REVERT: M 80 TYR cc_start: 0.7242 (m-80) cc_final: 0.7011 (m-80) outliers start: 94 outliers final: 59 residues processed: 393 average time/residue: 0.1517 time to fit residues: 91.1473 Evaluate side-chains 336 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 364 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 647 GLU 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 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 161 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 265 LEU 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 I residue 299 SER Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 314 ASP 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 198 THR Chi-restraints excluded: chain K residue 244 THR 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 545 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 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 314 ASP Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 186 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 226 optimal weight: 0.4980 chunk 188 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN F 114 GLN H 77 ASN L 591 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.195435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.169712 restraints weight = 29941.301| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.44 r_work: 0.3891 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20421 Z= 0.141 Angle : 0.757 11.336 27904 Z= 0.379 Chirality : 0.047 0.230 3306 Planarity : 0.004 0.049 3430 Dihedral : 9.879 78.262 3905 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.64 % Favored : 95.07 % Rotamer: Outliers : 3.37 % Allowed : 16.30 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.16), residues: 2433 helix: -1.17 (0.26), residues: 399 sheet: -0.20 (0.22), residues: 531 loop : -1.67 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 432 TYR 0.014 0.001 TYR M 111 PHE 0.013 0.001 PHE K 391 TRP 0.019 0.001 TRP A 96 HIS 0.005 0.001 HIS K 105 Details of bonding type rmsd covalent geometry : bond 0.00308 (20315) covalent geometry : angle 0.72973 (27628) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.95174 ( 84) hydrogen bonds : bond 0.04367 ( 576) hydrogen bonds : angle 5.75766 ( 1557) link_ALPHA1-2 : bond 0.00695 ( 13) link_ALPHA1-2 : angle 1.64671 ( 39) link_ALPHA1-3 : bond 0.01201 ( 10) link_ALPHA1-3 : angle 1.97394 ( 30) link_ALPHA1-6 : bond 0.00505 ( 7) link_ALPHA1-6 : angle 1.50354 ( 21) link_BETA1-4 : bond 0.00405 ( 22) link_BETA1-4 : angle 3.00887 ( 66) link_NAG-ASN : bond 0.00128 ( 12) link_NAG-ASN : angle 1.72406 ( 36) *********************** 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 379 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7802 (m-30) cc_final: 0.7415 (m-30) REVERT: A 207 LYS cc_start: 0.7736 (tptt) cc_final: 0.7383 (tptt) REVERT: B 648 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7184 (mm-30) REVERT: B 652 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6639 (tm-30) REVERT: F 95 MET cc_start: 0.8036 (ttp) cc_final: 0.7729 (ttp) REVERT: F 112 TRP cc_start: 0.7533 (m100) cc_final: 0.7314 (m100) REVERT: F 231 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: F 345 VAL cc_start: 0.8478 (t) cc_final: 0.8092 (t) REVERT: G 540 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: G 648 GLU cc_start: 0.7591 (pt0) cc_final: 0.7254 (mm-30) REVERT: H 77 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: I 298 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7344 (tttp) REVERT: L 610 TRP cc_start: 0.7381 (t-100) cc_final: 0.6670 (t-100) REVERT: L 648 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7106 (mm-30) REVERT: M 80 TYR cc_start: 0.7017 (m-80) cc_final: 0.6768 (m-80) outliers start: 72 outliers final: 37 residues processed: 351 average time/residue: 0.1439 time to fit residues: 77.8149 Evaluate side-chains 303 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 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 573 ILE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain 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 218 CYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 394 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 K residue 104 MET Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain L residue 523 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 638 TYR Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 125 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 D 263 ASN F 262 ASN G 590 GLN H 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.191043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165702 restraints weight = 29665.490| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.56 r_work: 0.3858 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20421 Z= 0.203 Angle : 0.793 12.177 27904 Z= 0.393 Chirality : 0.048 0.279 3306 Planarity : 0.004 0.044 3430 Dihedral : 9.535 77.961 3905 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 4.03 % Allowed : 17.00 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.16), residues: 2433 helix: -1.08 (0.26), residues: 401 sheet: -0.19 (0.22), residues: 544 loop : -1.66 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 166 TYR 0.036 0.002 TYR M 111 PHE 0.016 0.002 PHE K 376 TRP 0.023 0.002 TRP K 96 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00478 (20315) covalent geometry : angle 0.76408 (27628) SS BOND : bond 0.00431 ( 42) SS BOND : angle 2.33620 ( 84) hydrogen bonds : bond 0.04450 ( 576) hydrogen bonds : angle 5.73079 ( 1557) link_ALPHA1-2 : bond 0.00682 ( 13) link_ALPHA1-2 : angle 1.64699 ( 39) link_ALPHA1-3 : bond 0.01084 ( 10) link_ALPHA1-3 : angle 2.03304 ( 30) link_ALPHA1-6 : bond 0.00255 ( 7) link_ALPHA1-6 : angle 1.61340 ( 21) link_BETA1-4 : bond 0.00514 ( 22) link_BETA1-4 : angle 2.92637 ( 66) link_NAG-ASN : bond 0.00317 ( 12) link_NAG-ASN : angle 1.75189 ( 36) *********************** 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 361 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8020 (m-30) cc_final: 0.7682 (m-30) REVERT: A 207 LYS cc_start: 0.7631 (tptt) cc_final: 0.7249 (tptt) REVERT: B 648 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7141 (mm-30) REVERT: B 652 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6822 (tm-30) REVERT: F 95 MET cc_start: 0.7948 (ttp) cc_final: 0.7632 (ttp) REVERT: F 231 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: F 345 VAL cc_start: 0.8527 (t) cc_final: 0.8145 (t) REVERT: G 648 GLU cc_start: 0.7629 (pt0) cc_final: 0.7284 (mm-30) REVERT: H 80 TYR cc_start: 0.7161 (m-80) cc_final: 0.6861 (m-80) REVERT: H 81 MET cc_start: 0.7842 (ttp) cc_final: 0.7420 (ttp) REVERT: K 107 ASP cc_start: 0.7909 (m-30) cc_final: 0.7471 (m-30) REVERT: K 114 GLN cc_start: 0.7439 (mt0) cc_final: 0.6814 (tt0) REVERT: L 610 TRP cc_start: 0.7529 (t-100) cc_final: 0.6638 (t-100) REVERT: L 648 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6972 (mm-30) REVERT: M 80 TYR cc_start: 0.7088 (m-80) cc_final: 0.6555 (m-80) outliers start: 86 outliers final: 65 residues processed: 332 average time/residue: 0.1471 time to fit residues: 74.8137 Evaluate side-chains 326 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 260 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 198 THR 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 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 189 SER 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 630 GLN Chi-restraints excluded: chain L residue 638 TYR Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain N residue 253 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 86 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 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 650 GLN G 540 GLN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.187953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.163186 restraints weight = 29552.444| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.45 r_work: 0.3819 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20421 Z= 0.247 Angle : 0.833 14.016 27904 Z= 0.411 Chirality : 0.049 0.280 3306 Planarity : 0.005 0.059 3430 Dihedral : 9.606 79.076 3905 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.74 % Favored : 92.97 % Rotamer: Outliers : 4.87 % Allowed : 17.33 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2433 helix: -0.93 (0.26), residues: 384 sheet: -0.39 (0.22), residues: 559 loop : -1.71 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.041 0.002 TYR M 111 PHE 0.016 0.002 PHE D 319 TRP 0.029 0.002 TRP K 96 HIS 0.005 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00586 (20315) covalent geometry : angle 0.80838 (27628) SS BOND : bond 0.00587 ( 42) SS BOND : angle 2.07325 ( 84) hydrogen bonds : bond 0.04546 ( 576) hydrogen bonds : angle 5.80101 ( 1557) link_ALPHA1-2 : bond 0.00748 ( 13) link_ALPHA1-2 : angle 1.61360 ( 39) link_ALPHA1-3 : bond 0.00993 ( 10) link_ALPHA1-3 : angle 2.03087 ( 30) link_ALPHA1-6 : bond 0.00250 ( 7) link_ALPHA1-6 : angle 1.77164 ( 21) link_BETA1-4 : bond 0.00504 ( 22) link_BETA1-4 : angle 2.85901 ( 66) link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 1.91467 ( 36) *********************** 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 393 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 289 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8113 (m-30) cc_final: 0.7807 (m-30) REVERT: B 648 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7163 (mm-30) REVERT: B 652 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6894 (tm-30) REVERT: B 661 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6310 (mt) REVERT: F 95 MET cc_start: 0.7909 (ttp) cc_final: 0.7618 (ttp) REVERT: F 231 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: F 345 VAL cc_start: 0.8566 (t) cc_final: 0.8203 (t) REVERT: G 648 GLU cc_start: 0.7648 (pt0) cc_final: 0.7327 (mm-30) REVERT: H 80 TYR cc_start: 0.7401 (m-80) cc_final: 0.7148 (m-80) REVERT: H 81 MET cc_start: 0.7919 (ttp) cc_final: 0.7673 (ttp) REVERT: H 110 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8131 (p90) REVERT: K 49 LYS cc_start: 0.7643 (tptt) cc_final: 0.7387 (tttp) REVERT: K 107 ASP cc_start: 0.7922 (m-30) cc_final: 0.7488 (m-30) REVERT: K 114 GLN cc_start: 0.7469 (mt0) cc_final: 0.6864 (tt0) REVERT: L 610 TRP cc_start: 0.7305 (t-100) cc_final: 0.6614 (t-100) REVERT: L 648 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6959 (mm-30) REVERT: M 80 TYR cc_start: 0.7211 (m-80) cc_final: 0.6720 (m-80) outliers start: 104 outliers final: 87 residues processed: 359 average time/residue: 0.1476 time to fit residues: 81.1293 Evaluate side-chains 359 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 269 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 161 THR 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 247 CYS 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 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 234 LEU 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 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 198 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain G residue 660 LEU 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 110 TYR 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 305 LEU 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 165 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 209 THR 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 630 GLN Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 638 TYR Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 59 ILE 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 178 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** H 77 ASN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.192047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167007 restraints weight = 29798.797| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.56 r_work: 0.3846 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20421 Z= 0.144 Angle : 0.716 10.172 27904 Z= 0.353 Chirality : 0.045 0.228 3306 Planarity : 0.004 0.059 3430 Dihedral : 8.738 71.930 3905 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.47 % Favored : 94.29 % Rotamer: Outliers : 4.31 % Allowed : 18.36 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.16), residues: 2433 helix: -0.73 (0.27), residues: 395 sheet: -0.21 (0.21), residues: 582 loop : -1.58 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 166 TYR 0.021 0.001 TYR M 111 PHE 0.009 0.001 PHE D 319 TRP 0.043 0.002 TRP K 96 HIS 0.005 0.001 HIS K 105 Details of bonding type rmsd covalent geometry : bond 0.00330 (20315) covalent geometry : angle 0.69331 (27628) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.54061 ( 84) hydrogen bonds : bond 0.03859 ( 576) hydrogen bonds : angle 5.45281 ( 1557) link_ALPHA1-2 : bond 0.00640 ( 13) link_ALPHA1-2 : angle 1.57631 ( 39) link_ALPHA1-3 : bond 0.01040 ( 10) link_ALPHA1-3 : angle 1.84943 ( 30) link_ALPHA1-6 : bond 0.00355 ( 7) link_ALPHA1-6 : angle 1.56453 ( 21) link_BETA1-4 : bond 0.00407 ( 22) link_BETA1-4 : angle 2.66279 ( 66) link_NAG-ASN : bond 0.00118 ( 12) link_NAG-ASN : angle 1.57208 ( 36) *********************** 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 384 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 292 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8062 (m-30) cc_final: 0.7733 (m-30) REVERT: A 165 ILE cc_start: 0.8044 (mm) cc_final: 0.7648 (mt) REVERT: B 648 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7193 (mm-30) REVERT: B 650 GLN cc_start: 0.8134 (tp40) cc_final: 0.7861 (tm-30) REVERT: B 652 GLN cc_start: 0.7245 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 661 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6448 (mt) REVERT: F 95 MET cc_start: 0.7810 (ttp) cc_final: 0.7570 (ttp) REVERT: F 345 VAL cc_start: 0.8493 (t) cc_final: 0.8126 (t) REVERT: G 540 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: G 648 GLU cc_start: 0.7601 (pt0) cc_final: 0.7271 (mm-30) REVERT: H 80 TYR cc_start: 0.7344 (m-80) cc_final: 0.7125 (m-80) REVERT: H 81 MET cc_start: 0.7806 (ttp) cc_final: 0.7580 (ttp) REVERT: K 49 LYS cc_start: 0.7464 (tptt) cc_final: 0.7229 (tttp) REVERT: K 107 ASP cc_start: 0.7895 (m-30) cc_final: 0.7460 (m-30) REVERT: K 114 GLN cc_start: 0.7387 (mt0) cc_final: 0.6810 (tt0) REVERT: L 610 TRP cc_start: 0.7363 (t-100) cc_final: 0.6696 (t-100) REVERT: L 648 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6965 (mm-30) REVERT: M 80 TYR cc_start: 0.7138 (m-80) cc_final: 0.6872 (m-80) outliers start: 92 outliers final: 60 residues processed: 354 average time/residue: 0.1488 time to fit residues: 81.4292 Evaluate side-chains 333 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 265 LEU 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 394 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 209 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 394 THR 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 G residue 660 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 69 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 120 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 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 573 ILE Chi-restraints excluded: chain L residue 638 TYR Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 264 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 82 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 151 optimal weight: 0.0000 chunk 146 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 658 GLN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN L 650 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.193464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168440 restraints weight = 29979.687| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.58 r_work: 0.3897 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20421 Z= 0.130 Angle : 0.697 10.094 27904 Z= 0.344 Chirality : 0.045 0.268 3306 Planarity : 0.004 0.044 3430 Dihedral : 8.253 70.232 3905 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.88 % Favored : 93.88 % Rotamer: Outliers : 3.51 % Allowed : 19.39 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.17), residues: 2433 helix: -0.57 (0.27), residues: 401 sheet: -0.20 (0.21), residues: 583 loop : -1.44 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 166 TYR 0.020 0.001 TYR C 111 PHE 0.008 0.001 PHE D 319 TRP 0.056 0.002 TRP K 96 HIS 0.005 0.001 HIS K 105 Details of bonding type rmsd covalent geometry : bond 0.00292 (20315) covalent geometry : angle 0.67544 (27628) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.50676 ( 84) hydrogen bonds : bond 0.03648 ( 576) hydrogen bonds : angle 5.22908 ( 1557) link_ALPHA1-2 : bond 0.00626 ( 13) link_ALPHA1-2 : angle 1.58265 ( 39) link_ALPHA1-3 : bond 0.00965 ( 10) link_ALPHA1-3 : angle 1.82032 ( 30) link_ALPHA1-6 : bond 0.00443 ( 7) link_ALPHA1-6 : angle 1.49753 ( 21) link_BETA1-4 : bond 0.00411 ( 22) link_BETA1-4 : angle 2.54844 ( 66) link_NAG-ASN : bond 0.00052 ( 12) link_NAG-ASN : angle 1.46306 ( 36) *********************** 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 373 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8006 (m-30) cc_final: 0.7644 (m-30) REVERT: A 165 ILE cc_start: 0.8010 (mm) cc_final: 0.7652 (mt) REVERT: B 648 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7117 (mm-30) REVERT: B 650 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7715 (tm-30) REVERT: B 652 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6967 (tm-30) REVERT: F 107 ASP cc_start: 0.8121 (m-30) cc_final: 0.7781 (m-30) REVERT: F 345 VAL cc_start: 0.8478 (t) cc_final: 0.8115 (t) REVERT: G 540 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: G 648 GLU cc_start: 0.7471 (pt0) cc_final: 0.7054 (mm-30) REVERT: H 80 TYR cc_start: 0.7175 (m-80) cc_final: 0.6942 (m-80) REVERT: K 49 LYS cc_start: 0.7516 (tptt) cc_final: 0.7290 (tttp) REVERT: K 107 ASP cc_start: 0.7884 (m-30) cc_final: 0.7468 (m-30) REVERT: L 610 TRP cc_start: 0.7454 (t-100) cc_final: 0.6773 (t-100) REVERT: L 648 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7156 (mm-30) REVERT: M 80 TYR cc_start: 0.7122 (m-80) cc_final: 0.6857 (m-80) REVERT: M 84 ARG cc_start: 0.7005 (mpp80) cc_final: 0.6524 (mpt180) outliers start: 75 outliers final: 58 residues processed: 347 average time/residue: 0.1423 time to fit residues: 76.3326 Evaluate side-chains 345 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 189 SER 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 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 234 LEU 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 184 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 182 VAL 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 L residue 523 LEU Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 264 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 219 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.168831 restraints weight = 29743.572| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.56 r_work: 0.3900 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20421 Z= 0.129 Angle : 0.695 13.536 27904 Z= 0.342 Chirality : 0.045 0.238 3306 Planarity : 0.004 0.045 3430 Dihedral : 8.069 69.339 3905 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.22 % Favored : 94.53 % Rotamer: Outliers : 3.37 % Allowed : 19.95 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.17), residues: 2433 helix: -0.49 (0.27), residues: 401 sheet: -0.13 (0.22), residues: 583 loop : -1.37 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 166 TYR 0.020 0.001 TYR C 111 PHE 0.008 0.001 PHE D 319 TRP 0.054 0.001 TRP A 96 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00293 (20315) covalent geometry : angle 0.67490 (27628) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.46921 ( 84) hydrogen bonds : bond 0.03597 ( 576) hydrogen bonds : angle 5.13331 ( 1557) link_ALPHA1-2 : bond 0.00590 ( 13) link_ALPHA1-2 : angle 1.55839 ( 39) link_ALPHA1-3 : bond 0.00955 ( 10) link_ALPHA1-3 : angle 1.77746 ( 30) link_ALPHA1-6 : bond 0.00456 ( 7) link_ALPHA1-6 : angle 1.49530 ( 21) link_BETA1-4 : bond 0.00411 ( 22) link_BETA1-4 : angle 2.48609 ( 66) link_NAG-ASN : bond 0.00056 ( 12) link_NAG-ASN : angle 1.40808 ( 36) *********************** 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 361 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 289 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8385 (m100) cc_final: 0.8129 (m100) REVERT: A 107 ASP cc_start: 0.8042 (m-30) cc_final: 0.7712 (m-30) REVERT: A 114 GLN cc_start: 0.7151 (tt0) cc_final: 0.6464 (tt0) REVERT: A 165 ILE cc_start: 0.8032 (mm) cc_final: 0.7667 (mt) REVERT: B 648 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7117 (mm-30) REVERT: B 650 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7711 (tm-30) REVERT: B 652 GLN cc_start: 0.7255 (tm-30) cc_final: 0.6992 (tm-30) REVERT: F 107 ASP cc_start: 0.8207 (m-30) cc_final: 0.7827 (m-30) REVERT: F 345 VAL cc_start: 0.8440 (t) cc_final: 0.8060 (t) REVERT: G 540 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: G 648 GLU cc_start: 0.7447 (pt0) cc_final: 0.7030 (mm-30) REVERT: H 80 TYR cc_start: 0.7205 (m-80) cc_final: 0.6976 (m-80) REVERT: K 107 ASP cc_start: 0.7872 (m-30) cc_final: 0.7444 (m-30) REVERT: L 610 TRP cc_start: 0.7414 (t-100) cc_final: 0.6759 (t-100) REVERT: L 648 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7178 (mm-30) REVERT: M 80 TYR cc_start: 0.7160 (m-80) cc_final: 0.6869 (m-80) REVERT: M 84 ARG cc_start: 0.7046 (mpp80) cc_final: 0.6583 (mpt180) REVERT: M 115 ASP cc_start: 0.7274 (t0) cc_final: 0.7071 (t0) outliers start: 72 outliers final: 62 residues processed: 337 average time/residue: 0.1365 time to fit residues: 71.0943 Evaluate side-chains 342 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 234 LEU 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 184 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 213 ILE 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 L residue 523 LEU Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 59 ILE 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 163 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 0.0980 chunk 166 optimal weight: 0.0370 chunk 99 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 overall best weight: 1.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.194697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.169588 restraints weight = 29897.784| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.61 r_work: 0.3877 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20421 Z= 0.124 Angle : 0.687 13.634 27904 Z= 0.338 Chirality : 0.045 0.218 3306 Planarity : 0.004 0.046 3430 Dihedral : 7.741 66.265 3905 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % Rotamer: Outliers : 3.51 % Allowed : 20.09 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2433 helix: -0.43 (0.27), residues: 407 sheet: -0.05 (0.22), residues: 577 loop : -1.27 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 166 TYR 0.027 0.001 TYR C 111 PHE 0.010 0.001 PHE C 114 TRP 0.053 0.001 TRP A 96 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00280 (20315) covalent geometry : angle 0.66870 (27628) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.35724 ( 84) hydrogen bonds : bond 0.03466 ( 576) hydrogen bonds : angle 5.02442 ( 1557) link_ALPHA1-2 : bond 0.00570 ( 13) link_ALPHA1-2 : angle 1.53804 ( 39) link_ALPHA1-3 : bond 0.00962 ( 10) link_ALPHA1-3 : angle 1.72006 ( 30) link_ALPHA1-6 : bond 0.00523 ( 7) link_ALPHA1-6 : angle 1.46294 ( 21) link_BETA1-4 : bond 0.00408 ( 22) link_BETA1-4 : angle 2.40632 ( 66) link_NAG-ASN : bond 0.00044 ( 12) link_NAG-ASN : angle 1.32858 ( 36) ********************** 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 364 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 289 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8058 (m-30) cc_final: 0.7759 (m-30) REVERT: A 114 GLN cc_start: 0.7170 (tt0) cc_final: 0.6452 (tt0) REVERT: A 165 ILE cc_start: 0.8091 (mm) cc_final: 0.7838 (mm) REVERT: B 648 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7177 (mm-30) REVERT: B 650 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7771 (tm-30) REVERT: B 652 GLN cc_start: 0.7312 (tm-30) cc_final: 0.7089 (tm-30) REVERT: F 107 ASP cc_start: 0.8233 (m-30) cc_final: 0.7865 (m-30) REVERT: F 345 VAL cc_start: 0.8403 (t) cc_final: 0.8008 (t) REVERT: G 540 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: G 648 GLU cc_start: 0.7423 (pt0) cc_final: 0.7056 (mm-30) REVERT: H 80 TYR cc_start: 0.7182 (m-80) cc_final: 0.6944 (m-80) REVERT: L 610 TRP cc_start: 0.7347 (t-100) cc_final: 0.6772 (t-100) REVERT: L 648 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7241 (mm-30) REVERT: M 80 TYR cc_start: 0.7154 (m-80) cc_final: 0.6824 (m-80) REVERT: M 84 ARG cc_start: 0.7060 (mpp80) cc_final: 0.6592 (mpt180) REVERT: N 234 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5747 (tt) outliers start: 75 outliers final: 63 residues processed: 339 average time/residue: 0.1390 time to fit residues: 72.8791 Evaluate side-chains 343 residues out of total 2135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain D residue 234 LEU 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 184 LEU Chi-restraints excluded: chain F residue 188 THR 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 254 VAL Chi-restraints excluded: chain F residue 258 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 534 SER Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 182 VAL 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 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 L residue 523 LEU Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 322 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 48 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN L 577 GLN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.190815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165739 restraints weight = 29530.524| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.56 r_work: 0.3840 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20421 Z= 0.202 Angle : 0.775 13.501 27904 Z= 0.382 Chirality : 0.047 0.259 3306 Planarity : 0.005 0.049 3430 Dihedral : 8.485 71.621 3905 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.82 % Favored : 92.93 % Rotamer: Outliers : 3.65 % Allowed : 20.05 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.17), residues: 2433 helix: -0.61 (0.26), residues: 408 sheet: -0.11 (0.22), residues: 559 loop : -1.40 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 98 TYR 0.043 0.002 TYR C 111 PHE 0.016 0.002 PHE H 114 TRP 0.039 0.002 TRP A 96 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00477 (20315) covalent geometry : angle 0.75440 (27628) SS BOND : bond 0.00465 ( 42) SS BOND : angle 1.75330 ( 84) hydrogen bonds : bond 0.04042 ( 576) hydrogen bonds : angle 5.32623 ( 1557) link_ALPHA1-2 : bond 0.00670 ( 13) link_ALPHA1-2 : angle 1.59343 ( 39) link_ALPHA1-3 : bond 0.00808 ( 10) link_ALPHA1-3 : angle 1.85630 ( 30) link_ALPHA1-6 : bond 0.00241 ( 7) link_ALPHA1-6 : angle 1.68814 ( 21) link_BETA1-4 : bond 0.00456 ( 22) link_BETA1-4 : angle 2.50653 ( 66) link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 1.57716 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.77 seconds wall clock time: 77 minutes 0.26 seconds (4620.26 seconds total)