Starting phenix.real_space_refine on Tue May 20 10:01:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8saz_40285/05_2025/8saz_40285_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8saz_40285/05_2025/8saz_40285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8saz_40285/05_2025/8saz_40285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8saz_40285/05_2025/8saz_40285.map" model { file = "/net/cci-nas-00/data/ceres_data/8saz_40285/05_2025/8saz_40285_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8saz_40285/05_2025/8saz_40285_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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 132 5.16 5 C 12453 2.51 5 N 3327 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19960 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" 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: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "O" 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: "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: 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: "R" 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: "S" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "T" 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: "U" 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: "V" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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 Time building chain proxies: 11.40, per 1000 atoms: 0.57 Number of scatterers: 19960 At special positions: 0 Unit cell: (158.36, 161.57, 139.1, 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 132 16.00 O 4048 8.00 N 3327 7.00 C 12453 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=2.04 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=2.03 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=2.02 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=2.03 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=2.03 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 22 " - pdb=" SG CYS D 90 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 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 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 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=2.03 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=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " 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 G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 10 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 10 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " " BMA J 3 " - " MAN J 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 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 U 2 " - " BMA U 3 " " 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 X 2 " - " BMA X 3 " NAG-ASN " NAG G 1 " - " ASN E 332 " " NAG J 1 " - " ASN E 301 " " NAG O 1 " - " ASN E 156 " " NAG P 1 " - " ASN E 442 " " NAG Q 1 " - " ASN K 301 " " NAG R 1 " - " ASN K 156 " " NAG S 1 " - " ASN K 332 " " NAG T 1 " - " ASN K 442 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 156 " " NAG X 1 " - " ASN A 442 " Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 2.5 seconds 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 33 sheets defined 20.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.786A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 62 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.370A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 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 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.693A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.879A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 594 removed outlier: 4.096A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.994A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 654 removed outlier: 3.720A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 4.004A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.710A pdb=" N ALA E 60 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.364A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.508A pdb=" N GLU E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.016A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 594 removed outlier: 4.085A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 597 No H-bonds generated for 'chain 'F' and resid 595 through 597' Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.043A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.714A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 660 removed outlier: 3.908A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.809A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU K 62 " --> pdb=" O ARG K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.438A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 3.665A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (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 335 through 350 Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 474 through 481 removed outlier: 4.186A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 535 removed outlier: 4.164A pdb=" N MET L 535 " --> pdb=" O GLY L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 542 removed outlier: 4.083A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 4.058A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP L 589 " --> pdb=" O ARG L 585 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE L 595 " --> pdb=" O GLN L 591 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 635 removed outlier: 4.073A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 660 removed outlier: 3.732A pdb=" N ILE L 642 " --> pdb=" O TYR L 638 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN L 650 " --> pdb=" O LEU L 646 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS L 655 " --> pdb=" O ASN L 651 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU L 657 " --> pdb=" O GLN L 653 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN L 658 " --> pdb=" O GLU L 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.531A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 4.699A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.215A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.700A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 382 through 386 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.757A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.602A pdb=" N THR C 121 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.848A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.468A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.324A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.787A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AB7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.242A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.717A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 386 current: chain 'E' and resid 467 through 470 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 11 current: chain 'H' and resid 45 through 51 removed outlier: 3.602A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 116 through 117 Processing sheet with id=AC2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.555A pdb=" N VAL I 10 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 23 Processing sheet with id=AC4, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.264A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL L 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL K 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR L 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR K 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS L 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 45 through 46 removed outlier: 4.058A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.798A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 169 through 176 Processing sheet with id=AC9, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.244A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 261 current: chain 'K' and resid 284 through 308 removed outlier: 6.700A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 316 through 323 current: chain 'K' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 382 through 386 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD2, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.739A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.502A pdb=" N THR M 121 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.535A pdb=" N VAL N 10 " --> pdb=" O LYS N 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.559A pdb=" N SER N 67 " --> pdb=" O SER N 74 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 46 through 51 removed outlier: 6.510A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL N 35 " --> pdb=" O TYR N 51 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 6.89 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: 6311 1.35 - 1.48: 5347 1.48 - 1.61: 8536 1.61 - 1.73: 3 1.73 - 1.86: 177 Bond restraints: 20374 Sorted by residual: bond pdb=" C1 MAN G 8 " pdb=" C2 MAN G 8 " ideal model delta sigma weight residual 1.526 1.613 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN S 8 " pdb=" C2 MAN S 8 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 MAN V 8 " pdb=" C2 MAN V 8 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CG PRO I 57 " pdb=" CD PRO I 57 " ideal model delta sigma weight residual 1.503 1.366 0.137 3.40e-02 8.65e+02 1.63e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.483 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 20369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 27394 3.82 - 7.64: 274 7.64 - 11.46: 27 11.46 - 15.28: 2 15.28 - 19.11: 2 Bond angle restraints: 27699 Sorted by residual: angle pdb=" N PRO I 57 " pdb=" CD PRO I 57 " pdb=" CG PRO I 57 " ideal model delta sigma weight residual 103.20 84.09 19.11 1.50e+00 4.44e-01 1.62e+02 angle pdb=" CA PRO I 57 " pdb=" CB PRO I 57 " pdb=" CG PRO I 57 " ideal model delta sigma weight residual 104.50 88.15 16.35 1.90e+00 2.77e-01 7.40e+01 angle pdb=" N PRO D 57 " pdb=" CD PRO D 57 " pdb=" CG PRO D 57 " ideal model delta sigma weight residual 103.20 90.68 12.52 1.50e+00 4.44e-01 6.96e+01 angle pdb=" CA PRO D 57 " pdb=" CB PRO D 57 " pdb=" CG PRO D 57 " ideal model delta sigma weight residual 104.50 92.14 12.36 1.90e+00 2.77e-01 4.23e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 131.15 -9.45 1.80e+00 3.09e-01 2.75e+01 ... (remaining 27694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.44: 12104 22.44 - 44.88: 678 44.88 - 67.32: 103 67.32 - 89.76: 96 89.76 - 112.20: 47 Dihedral angle restraints: 13028 sinusoidal: 5924 harmonic: 7104 Sorted by residual: dihedral pdb=" CA CYS K 196 " pdb=" C CYS K 196 " pdb=" N ASN K 197 " pdb=" CA ASN K 197 " ideal model delta harmonic sigma weight residual 180.00 145.55 34.45 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA VAL B 570 " pdb=" C VAL B 570 " pdb=" N TRP B 571 " pdb=" CA TRP B 571 " ideal model delta harmonic sigma weight residual 180.00 147.95 32.05 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -31.13 -54.87 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 13025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2700 0.062 - 0.124: 473 0.124 - 0.186: 112 0.186 - 0.248: 3 0.248 - 0.311: 13 Chirality restraints: 3301 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 156 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3298 not shown) Planarity restraints: 3453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 56 " -0.581 9.50e-02 1.11e+02 2.60e-01 4.16e+01 pdb=" NE ARG N 56 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG N 56 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG N 56 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG N 56 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 116 " 0.016 2.00e-02 2.50e+03 1.83e-02 6.71e+00 pdb=" CG TYR M 116 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR M 116 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR M 116 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 116 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR M 116 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR M 116 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR M 116 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 106 " -0.022 2.00e-02 2.50e+03 1.48e-02 4.39e+00 pdb=" CG TYR C 106 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 106 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 106 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 106 " -0.006 2.00e-02 2.50e+03 ... (remaining 3450 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 837 2.71 - 3.26: 19898 3.26 - 3.81: 29852 3.81 - 4.35: 38089 4.35 - 4.90: 65567 Nonbonded interactions: 154243 Sorted by model distance: nonbonded pdb=" OG1 THR K 163 " pdb=" OE1 GLU K 164 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR A 163 " pdb=" OE1 GLU A 164 " model vdw 2.183 3.040 nonbonded pdb=" OG SER N 69 " pdb=" O THR N 72 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG K 456 " pdb=" OE1 GLU K 466 " model vdw 2.208 3.120 nonbonded pdb=" O TRP B 571 " pdb=" NE2 GLN B 575 " model vdw 2.219 3.120 ... (remaining 154238 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'F' 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 'G' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 44.750 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.120 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 0.137 20481 Z= 0.286 Angle : 1.048 19.105 27978 Z= 0.515 Chirality : 0.054 0.311 3301 Planarity : 0.007 0.260 3441 Dihedral : 17.303 112.199 8360 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.17), residues: 2442 helix: -1.35 (0.24), residues: 429 sheet: -1.32 (0.21), residues: 615 loop : -1.13 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 427 HIS 0.008 0.002 HIS E 330 PHE 0.034 0.002 PHE I 64 TYR 0.045 0.002 TYR M 116 ARG 0.012 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 3.27868 ( 36) link_ALPHA1-6 : bond 0.01209 ( 8) link_ALPHA1-6 : angle 3.63579 ( 24) link_BETA1-4 : bond 0.01132 ( 24) link_BETA1-4 : angle 4.70279 ( 72) link_ALPHA1-2 : bond 0.01478 ( 9) link_ALPHA1-2 : angle 6.43525 ( 27) link_ALPHA1-3 : bond 0.01087 ( 12) link_ALPHA1-3 : angle 3.94848 ( 36) hydrogen bonds : bond 0.24209 ( 518) hydrogen bonds : angle 9.64635 ( 1353) SS BOND : bond 0.00533 ( 42) SS BOND : angle 1.66382 ( 84) covalent geometry : bond 0.00599 (20374) covalent geometry : angle 0.97879 (27699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 745 time to evaluate : 2.073 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7681 (ptpt) cc_final: 0.7303 (ttmm) REVERT: A 217 TYR cc_start: 0.7582 (m-80) cc_final: 0.7155 (m-80) REVERT: B 607 ASN cc_start: 0.8372 (p0) cc_final: 0.8158 (p0) REVERT: B 659 ASP cc_start: 0.8091 (m-30) cc_final: 0.7824 (m-30) REVERT: C 91 THR cc_start: 0.8163 (m) cc_final: 0.7946 (t) REVERT: D 25 THR cc_start: 0.8366 (t) cc_final: 0.8121 (p) REVERT: D 35 VAL cc_start: 0.9009 (t) cc_final: 0.8786 (p) REVERT: D 71 ASN cc_start: 0.7594 (m-40) cc_final: 0.7385 (t0) REVERT: D 89 TYR cc_start: 0.8125 (m-80) cc_final: 0.7534 (m-80) REVERT: E 104 MET cc_start: 0.9010 (ttt) cc_final: 0.8787 (ttp) REVERT: E 121 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7270 (ttmm) REVERT: E 201 CYS cc_start: 0.5711 (m) cc_final: 0.4403 (m) REVERT: E 217 TYR cc_start: 0.7678 (m-80) cc_final: 0.7421 (m-80) REVERT: F 534 SER cc_start: 0.9393 (t) cc_final: 0.9150 (p) REVERT: F 602 LEU cc_start: 0.8622 (pt) cc_final: 0.8336 (pp) REVERT: F 610 TRP cc_start: 0.8454 (t-100) cc_final: 0.8078 (t-100) REVERT: H 101 TRP cc_start: 0.8527 (t60) cc_final: 0.8320 (t-100) REVERT: I 35 VAL cc_start: 0.9046 (t) cc_final: 0.8834 (p) REVERT: I 77 ILE cc_start: 0.8766 (mt) cc_final: 0.8425 (mt) REVERT: I 89 TYR cc_start: 0.8214 (m-80) cc_final: 0.7429 (m-80) REVERT: K 121 LYS cc_start: 0.7643 (ptpt) cc_final: 0.7292 (ttmm) REVERT: L 534 SER cc_start: 0.9418 (t) cc_final: 0.9116 (p) REVERT: L 545 LEU cc_start: 0.6637 (tp) cc_final: 0.6198 (tt) REVERT: L 631 TRP cc_start: 0.8854 (t-100) cc_final: 0.8569 (t-100) REVERT: L 659 ASP cc_start: 0.7798 (m-30) cc_final: 0.7591 (m-30) REVERT: M 4 LEU cc_start: 0.8512 (mm) cc_final: 0.8236 (mp) REVERT: N 25 THR cc_start: 0.8504 (t) cc_final: 0.8127 (p) REVERT: N 89 TYR cc_start: 0.8135 (m-80) cc_final: 0.7847 (m-80) outliers start: 3 outliers final: 0 residues processed: 745 average time/residue: 0.3244 time to fit residues: 360.0544 Evaluate side-chains 423 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 640 GLN C 6 GLN E 195 ASN E 302 ASN E 328 GLN E 374 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099384 restraints weight = 37260.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097896 restraints weight = 34635.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099363 restraints weight = 38621.547| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20481 Z= 0.300 Angle : 0.923 10.403 27978 Z= 0.454 Chirality : 0.053 0.283 3301 Planarity : 0.006 0.047 3441 Dihedral : 12.429 91.133 3941 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 4.03 % Allowed : 14.63 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2442 helix: -1.22 (0.25), residues: 408 sheet: -1.33 (0.19), residues: 717 loop : -1.16 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 338 HIS 0.010 0.003 HIS H 35 PHE 0.027 0.003 PHE K 233 TYR 0.022 0.003 TYR K 40 ARG 0.011 0.001 ARG K 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 12) link_NAG-ASN : angle 2.51658 ( 36) link_ALPHA1-6 : bond 0.00376 ( 8) link_ALPHA1-6 : angle 2.11008 ( 24) link_BETA1-4 : bond 0.00974 ( 24) link_BETA1-4 : angle 3.34651 ( 72) link_ALPHA1-2 : bond 0.00458 ( 9) link_ALPHA1-2 : angle 2.80589 ( 27) link_ALPHA1-3 : bond 0.01210 ( 12) link_ALPHA1-3 : angle 1.91210 ( 36) hydrogen bonds : bond 0.04877 ( 518) hydrogen bonds : angle 6.46998 ( 1353) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.54469 ( 84) covalent geometry : bond 0.00701 (20374) covalent geometry : angle 0.89409 (27699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 2.101 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: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8215 (ptpp) REVERT: A 121 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7547 (ttmm) REVERT: B 602 LEU cc_start: 0.8717 (pt) cc_final: 0.8392 (pp) REVERT: C 11 VAL cc_start: 0.8510 (t) cc_final: 0.8290 (m) REVERT: D 87 ASP cc_start: 0.7715 (t0) cc_final: 0.7386 (t0) REVERT: D 89 TYR cc_start: 0.7703 (m-80) cc_final: 0.7353 (m-80) REVERT: E 33 ASN cc_start: 0.7363 (p0) cc_final: 0.7077 (p0) REVERT: E 103 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7443 (mm110) REVERT: E 121 LYS cc_start: 0.7912 (ptpt) cc_final: 0.7587 (ttmm) REVERT: E 217 TYR cc_start: 0.8186 (m-80) cc_final: 0.7867 (m-80) REVERT: E 475 MET cc_start: 0.8388 (mmm) cc_final: 0.7097 (ptp) REVERT: F 602 LEU cc_start: 0.8803 (pt) cc_final: 0.8592 (pp) REVERT: F 646 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9130 (mm) REVERT: F 648 GLU cc_start: 0.8026 (pp20) cc_final: 0.7814 (tm-30) REVERT: H 101 TRP cc_start: 0.8789 (t60) cc_final: 0.8481 (t-100) REVERT: I 71 ASN cc_start: 0.8737 (m-40) cc_final: 0.8343 (t0) REVERT: K 121 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7699 (ttmm) REVERT: K 268 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7912 (mmmm) REVERT: K 502 LYS cc_start: 0.7632 (tptp) cc_final: 0.6760 (tptp) REVERT: L 542 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8254 (mtp-110) REVERT: L 577 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8430 (mm-40) REVERT: L 653 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8624 (tm-30) REVERT: M 12 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7804 (mmtp) REVERT: N 71 ASN cc_start: 0.8890 (m-40) cc_final: 0.8480 (t0) REVERT: N 85 GLU cc_start: 0.7097 (pt0) cc_final: 0.6666 (pt0) outliers start: 86 outliers final: 55 residues processed: 485 average time/residue: 0.3126 time to fit residues: 229.6502 Evaluate side-chains 413 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 347 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 317 PHE Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain L residue 538 THR Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 620 SER Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 223 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 157 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN B 640 GLN C 62 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 374 HIS F 658 GLN K 389 ASN L 640 GLN L 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098183 restraints weight = 37299.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.097166 restraints weight = 34840.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098393 restraints weight = 39544.869| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20481 Z= 0.221 Angle : 0.787 10.082 27978 Z= 0.383 Chirality : 0.048 0.302 3301 Planarity : 0.004 0.044 3441 Dihedral : 10.624 82.331 3941 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 4.08 % Allowed : 17.49 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2442 helix: -0.67 (0.26), residues: 408 sheet: -1.04 (0.20), residues: 699 loop : -1.14 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 101 HIS 0.019 0.002 HIS E 374 PHE 0.020 0.002 PHE K 317 TYR 0.017 0.002 TYR E 217 ARG 0.007 0.001 ARG K 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 12) link_NAG-ASN : angle 2.36343 ( 36) link_ALPHA1-6 : bond 0.00431 ( 8) link_ALPHA1-6 : angle 2.20032 ( 24) link_BETA1-4 : bond 0.00774 ( 24) link_BETA1-4 : angle 2.61103 ( 72) link_ALPHA1-2 : bond 0.00283 ( 9) link_ALPHA1-2 : angle 3.39715 ( 27) link_ALPHA1-3 : bond 0.01163 ( 12) link_ALPHA1-3 : angle 1.64858 ( 36) hydrogen bonds : bond 0.04207 ( 518) hydrogen bonds : angle 5.87187 ( 1353) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.53072 ( 84) covalent geometry : bond 0.00517 (20374) covalent geometry : angle 0.75757 (27699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 391 time to evaluate : 2.230 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: symmetry clash REVERT: A 201 CYS cc_start: 0.6429 (m) cc_final: 0.6070 (m) REVERT: B 542 ARG cc_start: 0.8443 (mtp-110) cc_final: 0.8229 (mtp-110) REVERT: B 602 LEU cc_start: 0.8773 (pt) cc_final: 0.8500 (pp) REVERT: B 653 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 660 LEU cc_start: 0.8208 (tp) cc_final: 0.7913 (tp) REVERT: C 11 VAL cc_start: 0.8431 (t) cc_final: 0.8168 (m) REVERT: D 87 ASP cc_start: 0.7302 (t0) cc_final: 0.7093 (t0) REVERT: E 33 ASN cc_start: 0.7465 (p0) cc_final: 0.7201 (p0) REVERT: E 103 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7569 (mm110) REVERT: E 475 MET cc_start: 0.8474 (mmm) cc_final: 0.7183 (ptp) REVERT: F 646 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8993 (mm) REVERT: F 653 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8888 (tm-30) REVERT: H 48 MET cc_start: 0.7428 (mmm) cc_final: 0.7073 (mmt) REVERT: H 101 TRP cc_start: 0.8863 (t60) cc_final: 0.8469 (t-100) REVERT: I 60 VAL cc_start: 0.6920 (t) cc_final: 0.6695 (m) REVERT: I 87 ASP cc_start: 0.7226 (t0) cc_final: 0.7024 (t0) REVERT: K 121 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7560 (ttmm) REVERT: K 217 TYR cc_start: 0.8092 (m-80) cc_final: 0.7518 (m-80) REVERT: K 502 LYS cc_start: 0.7459 (tptp) cc_final: 0.6720 (tptp) REVERT: L 542 ARG cc_start: 0.8584 (mtp-110) cc_final: 0.8298 (mtp-110) REVERT: L 543 ASN cc_start: 0.7862 (t0) cc_final: 0.7617 (t0) REVERT: L 653 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 87 outliers final: 53 residues processed: 445 average time/residue: 0.3055 time to fit residues: 209.4595 Evaluate side-chains 415 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 627 THR Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 163 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN B 658 GLN D 16 GLN E 374 HIS E 389 ASN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099158 restraints weight = 37429.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098782 restraints weight = 33281.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099716 restraints weight = 35732.104| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20481 Z= 0.149 Angle : 0.733 11.491 27978 Z= 0.357 Chirality : 0.047 0.305 3301 Planarity : 0.004 0.042 3441 Dihedral : 9.421 76.885 3941 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.08 % Favored : 94.72 % Rotamer: Outliers : 3.84 % Allowed : 18.66 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2442 helix: -0.56 (0.26), residues: 414 sheet: -0.79 (0.20), residues: 705 loop : -1.13 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 101 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.002 PHE I 64 TYR 0.017 0.001 TYR M 27 ARG 0.005 0.000 ARG N 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 12) link_NAG-ASN : angle 2.15680 ( 36) link_ALPHA1-6 : bond 0.00288 ( 8) link_ALPHA1-6 : angle 2.11823 ( 24) link_BETA1-4 : bond 0.00672 ( 24) link_BETA1-4 : angle 2.29042 ( 72) link_ALPHA1-2 : bond 0.00334 ( 9) link_ALPHA1-2 : angle 3.12980 ( 27) link_ALPHA1-3 : bond 0.01229 ( 12) link_ALPHA1-3 : angle 1.43503 ( 36) hydrogen bonds : bond 0.03499 ( 518) hydrogen bonds : angle 5.55767 ( 1353) SS BOND : bond 0.00288 ( 42) SS BOND : angle 1.56937 ( 84) covalent geometry : bond 0.00347 (20374) covalent geometry : angle 0.70676 (27699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 392 time to evaluate : 2.092 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: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.7481 (mpp) cc_final: 0.7188 (mpp) REVERT: B 542 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.8196 (mtp-110) REVERT: B 602 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (pp) REVERT: B 653 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8684 (tm-30) REVERT: B 660 LEU cc_start: 0.8366 (tp) cc_final: 0.8093 (tp) REVERT: C 11 VAL cc_start: 0.8423 (t) cc_final: 0.8203 (m) REVERT: D 89 TYR cc_start: 0.7752 (m-80) cc_final: 0.7537 (m-80) REVERT: E 33 ASN cc_start: 0.7567 (p0) cc_final: 0.7202 (p0) REVERT: E 475 MET cc_start: 0.8405 (mmm) cc_final: 0.7005 (ptp) REVERT: F 634 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7673 (mt-10) REVERT: F 646 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9003 (mm) REVERT: H 48 MET cc_start: 0.7273 (mmm) cc_final: 0.6975 (mmt) REVERT: H 101 TRP cc_start: 0.8876 (t60) cc_final: 0.8449 (t-100) REVERT: I 60 VAL cc_start: 0.7177 (t) cc_final: 0.6940 (m) REVERT: I 87 ASP cc_start: 0.7267 (t0) cc_final: 0.7012 (t0) REVERT: K 121 LYS cc_start: 0.7907 (ptpt) cc_final: 0.7417 (ttmm) REVERT: K 217 TYR cc_start: 0.8099 (m-80) cc_final: 0.7475 (m-80) REVERT: K 268 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8200 (mmmm) REVERT: L 542 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8294 (mtp-110) REVERT: L 543 ASN cc_start: 0.7956 (t0) cc_final: 0.7613 (t0) REVERT: L 648 GLU cc_start: 0.8194 (pp20) cc_final: 0.7761 (tp30) REVERT: L 653 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8578 (tm-30) REVERT: M 4 LEU cc_start: 0.8833 (mp) cc_final: 0.8622 (mp) REVERT: N 55 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8361 (mtpp) REVERT: N 105 THR cc_start: 0.8129 (m) cc_final: 0.7619 (p) outliers start: 82 outliers final: 55 residues processed: 438 average time/residue: 0.2969 time to fit residues: 201.9883 Evaluate side-chains 425 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 368 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 535 MET Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 601 LYS Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 140 optimal weight: 7.9990 chunk 46 optimal weight: 0.0570 chunk 219 optimal weight: 20.0000 chunk 239 optimal weight: 50.0000 chunk 217 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 658 GLN F 640 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097614 restraints weight = 37605.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097020 restraints weight = 33743.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097471 restraints weight = 35288.612| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20481 Z= 0.180 Angle : 0.743 11.522 27978 Z= 0.360 Chirality : 0.047 0.297 3301 Planarity : 0.004 0.041 3441 Dihedral : 8.947 73.750 3941 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.12 % Favored : 94.64 % Rotamer: Outliers : 4.31 % Allowed : 19.46 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2442 helix: -0.47 (0.26), residues: 411 sheet: -0.70 (0.20), residues: 705 loop : -1.16 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 101 HIS 0.025 0.002 HIS E 374 PHE 0.018 0.002 PHE I 64 TYR 0.019 0.002 TYR A 361 ARG 0.006 0.001 ARG N 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 2.18607 ( 36) link_ALPHA1-6 : bond 0.00276 ( 8) link_ALPHA1-6 : angle 2.11022 ( 24) link_BETA1-4 : bond 0.00694 ( 24) link_BETA1-4 : angle 2.21557 ( 72) link_ALPHA1-2 : bond 0.00329 ( 9) link_ALPHA1-2 : angle 3.12424 ( 27) link_ALPHA1-3 : bond 0.01154 ( 12) link_ALPHA1-3 : angle 1.39837 ( 36) hydrogen bonds : bond 0.03488 ( 518) hydrogen bonds : angle 5.45244 ( 1353) SS BOND : bond 0.00460 ( 42) SS BOND : angle 1.75704 ( 84) covalent geometry : bond 0.00422 (20374) covalent geometry : angle 0.71617 (27699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 383 time to evaluate : 2.062 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: symmetry clash REVERT: A 33 ASN cc_start: 0.7364 (p0) cc_final: 0.6997 (p0) REVERT: B 535 MET cc_start: 0.7569 (mpp) cc_final: 0.7193 (mpp) REVERT: B 542 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8182 (mtp-110) REVERT: B 602 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8460 (pp) REVERT: B 660 LEU cc_start: 0.8502 (tp) cc_final: 0.8277 (tp) REVERT: D 68 LYS cc_start: 0.8347 (mtpt) cc_final: 0.8094 (tttp) REVERT: D 105 THR cc_start: 0.8147 (m) cc_final: 0.7548 (p) REVERT: E 33 ASN cc_start: 0.7595 (p0) cc_final: 0.7193 (p0) REVERT: E 475 MET cc_start: 0.8415 (mmm) cc_final: 0.7043 (ptp) REVERT: F 646 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9039 (mm) REVERT: F 650 GLN cc_start: 0.9142 (tp40) cc_final: 0.8051 (tm-30) REVERT: F 661 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7698 (mt) REVERT: H 10 GLU cc_start: 0.8428 (tp30) cc_final: 0.8138 (tp30) REVERT: H 48 MET cc_start: 0.7321 (mmm) cc_final: 0.7084 (mmm) REVERT: I 77 ILE cc_start: 0.9144 (pt) cc_final: 0.8577 (mm) REVERT: K 121 LYS cc_start: 0.8046 (ptpt) cc_final: 0.7651 (ttmm) REVERT: K 217 TYR cc_start: 0.8102 (m-80) cc_final: 0.7497 (m-80) REVERT: K 268 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8276 (mmmm) REVERT: L 543 ASN cc_start: 0.7954 (t0) cc_final: 0.7696 (t0) REVERT: M 4 LEU cc_start: 0.8792 (mp) cc_final: 0.8579 (mp) REVERT: N 55 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8540 (mtpp) REVERT: N 105 THR cc_start: 0.8162 (m) cc_final: 0.7626 (p) outliers start: 92 outliers final: 68 residues processed: 434 average time/residue: 0.2938 time to fit residues: 198.4604 Evaluate side-chains 430 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 359 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 601 LYS Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 627 THR Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 14 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 640 GLN F 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097576 restraints weight = 37543.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096554 restraints weight = 33483.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097576 restraints weight = 40030.419| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20481 Z= 0.178 Angle : 0.731 9.992 27978 Z= 0.353 Chirality : 0.046 0.292 3301 Planarity : 0.004 0.041 3441 Dihedral : 8.558 70.351 3941 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 4.59 % Allowed : 20.07 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2442 helix: -0.33 (0.27), residues: 411 sheet: -0.73 (0.20), residues: 720 loop : -1.12 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP M 101 HIS 0.005 0.001 HIS E 374 PHE 0.013 0.002 PHE E 353 TYR 0.017 0.002 TYR M 33 ARG 0.006 0.001 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 12) link_NAG-ASN : angle 2.13971 ( 36) link_ALPHA1-6 : bond 0.00316 ( 8) link_ALPHA1-6 : angle 2.08132 ( 24) link_BETA1-4 : bond 0.00666 ( 24) link_BETA1-4 : angle 2.12845 ( 72) link_ALPHA1-2 : bond 0.00274 ( 9) link_ALPHA1-2 : angle 3.12656 ( 27) link_ALPHA1-3 : bond 0.01167 ( 12) link_ALPHA1-3 : angle 1.36077 ( 36) hydrogen bonds : bond 0.03528 ( 518) hydrogen bonds : angle 5.28974 ( 1353) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.11107 ( 84) covalent geometry : bond 0.00415 (20374) covalent geometry : angle 0.70893 (27699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 369 time to evaluate : 2.091 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: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7538 (p0) cc_final: 0.7172 (p0) REVERT: B 542 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.8158 (mtp-110) REVERT: B 602 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 654 GLU cc_start: 0.8815 (tp30) cc_final: 0.8532 (tp30) REVERT: D 68 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8084 (tttp) REVERT: D 105 THR cc_start: 0.8019 (m) cc_final: 0.7402 (p) REVERT: E 33 ASN cc_start: 0.7564 (p0) cc_final: 0.7128 (p0) REVERT: E 164 GLU cc_start: 0.7100 (pm20) cc_final: 0.6812 (pt0) REVERT: E 317 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8533 (t80) REVERT: E 475 MET cc_start: 0.8335 (mmm) cc_final: 0.7051 (ptp) REVERT: F 633 LYS cc_start: 0.8942 (pptt) cc_final: 0.8668 (ptpp) REVERT: F 646 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9003 (mm) REVERT: F 647 GLU cc_start: 0.8102 (tt0) cc_final: 0.7763 (tt0) REVERT: H 48 MET cc_start: 0.7304 (mmm) cc_final: 0.7042 (mmm) REVERT: I 77 ILE cc_start: 0.8949 (pt) cc_final: 0.8642 (mm) REVERT: I 105 THR cc_start: 0.8566 (m) cc_final: 0.8020 (p) REVERT: K 121 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7733 (ttmm) REVERT: K 217 TYR cc_start: 0.8011 (m-80) cc_final: 0.7475 (m-80) REVERT: K 371 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8654 (tt) REVERT: K 501 CYS cc_start: 0.4986 (OUTLIER) cc_final: 0.4549 (t) REVERT: L 542 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8352 (ttp80) REVERT: M 4 LEU cc_start: 0.8845 (mp) cc_final: 0.8627 (mp) REVERT: M 70 MET cc_start: 0.8861 (mpp) cc_final: 0.8163 (mpt) REVERT: N 55 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8664 (mtpp) REVERT: N 105 THR cc_start: 0.8137 (m) cc_final: 0.7546 (p) outliers start: 98 outliers final: 78 residues processed: 428 average time/residue: 0.2978 time to fit residues: 198.5965 Evaluate side-chains 439 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 356 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 601 LYS Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 620 SER Chi-restraints excluded: chain L residue 627 THR Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 228 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 591 GLN F 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097781 restraints weight = 37556.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096276 restraints weight = 35293.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097355 restraints weight = 43251.846| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20481 Z= 0.175 Angle : 0.730 10.944 27978 Z= 0.351 Chirality : 0.046 0.291 3301 Planarity : 0.004 0.040 3441 Dihedral : 8.325 68.277 3941 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.68 % Rotamer: Outliers : 4.97 % Allowed : 20.07 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2442 helix: -0.28 (0.27), residues: 411 sheet: -0.67 (0.20), residues: 723 loop : -1.10 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 101 HIS 0.004 0.001 HIS E 330 PHE 0.013 0.001 PHE E 353 TYR 0.018 0.002 TYR E 361 ARG 0.007 0.000 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 2.11404 ( 36) link_ALPHA1-6 : bond 0.00375 ( 8) link_ALPHA1-6 : angle 2.07019 ( 24) link_BETA1-4 : bond 0.00651 ( 24) link_BETA1-4 : angle 2.09380 ( 72) link_ALPHA1-2 : bond 0.00343 ( 9) link_ALPHA1-2 : angle 3.09571 ( 27) link_ALPHA1-3 : bond 0.01138 ( 12) link_ALPHA1-3 : angle 1.32965 ( 36) hydrogen bonds : bond 0.03460 ( 518) hydrogen bonds : angle 5.18518 ( 1353) SS BOND : bond 0.00463 ( 42) SS BOND : angle 1.53364 ( 84) covalent geometry : bond 0.00409 (20374) covalent geometry : angle 0.70649 (27699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 369 time to evaluate : 2.451 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7347 (p0) cc_final: 0.7007 (p0) REVERT: B 542 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8118 (mtp-110) REVERT: B 602 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8077 (pp) REVERT: D 68 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8053 (tttp) REVERT: D 105 THR cc_start: 0.8066 (m) cc_final: 0.7425 (p) REVERT: E 33 ASN cc_start: 0.7599 (p0) cc_final: 0.7238 (p0) REVERT: E 164 GLU cc_start: 0.7139 (pm20) cc_final: 0.6871 (pt0) REVERT: E 317 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8432 (t80) REVERT: E 475 MET cc_start: 0.8331 (mmm) cc_final: 0.7154 (ptp) REVERT: F 622 ILE cc_start: 0.7547 (tp) cc_final: 0.7267 (tp) REVERT: F 633 LYS cc_start: 0.8912 (pptt) cc_final: 0.8685 (ptpp) REVERT: F 634 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7854 (mt-10) REVERT: F 661 LEU cc_start: 0.7965 (tt) cc_final: 0.7637 (tt) REVERT: H 48 MET cc_start: 0.7153 (mmm) cc_final: 0.6893 (mmm) REVERT: I 77 ILE cc_start: 0.8924 (pt) cc_final: 0.8623 (mm) REVERT: I 105 THR cc_start: 0.8597 (m) cc_final: 0.8092 (p) REVERT: K 121 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7770 (ttmm) REVERT: K 217 TYR cc_start: 0.8023 (m-80) cc_final: 0.7505 (m-80) REVERT: K 371 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (tt) REVERT: M 116 TYR cc_start: 0.8192 (m-80) cc_final: 0.7787 (m-10) REVERT: N 55 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8746 (mtpp) REVERT: N 68 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7857 (mtpp) REVERT: N 105 THR cc_start: 0.8143 (m) cc_final: 0.7635 (p) outliers start: 106 outliers final: 84 residues processed: 429 average time/residue: 0.3071 time to fit residues: 205.8953 Evaluate side-chains 438 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 186 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 242 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 0.0570 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN K 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096918 restraints weight = 37790.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095955 restraints weight = 38129.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096823 restraints weight = 46073.751| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20481 Z= 0.214 Angle : 0.764 10.660 27978 Z= 0.369 Chirality : 0.047 0.280 3301 Planarity : 0.004 0.043 3441 Dihedral : 8.307 67.435 3941 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.36 % Favored : 94.39 % Rotamer: Outliers : 4.83 % Allowed : 20.82 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2442 helix: -0.31 (0.26), residues: 411 sheet: -0.72 (0.19), residues: 744 loop : -1.16 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 101 HIS 0.005 0.002 HIS E 330 PHE 0.015 0.002 PHE K 376 TYR 0.020 0.002 TYR M 33 ARG 0.006 0.001 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 2.18570 ( 36) link_ALPHA1-6 : bond 0.00380 ( 8) link_ALPHA1-6 : angle 2.10353 ( 24) link_BETA1-4 : bond 0.00681 ( 24) link_BETA1-4 : angle 2.16295 ( 72) link_ALPHA1-2 : bond 0.00326 ( 9) link_ALPHA1-2 : angle 3.09829 ( 27) link_ALPHA1-3 : bond 0.01080 ( 12) link_ALPHA1-3 : angle 1.33906 ( 36) hydrogen bonds : bond 0.03708 ( 518) hydrogen bonds : angle 5.29007 ( 1353) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.29789 ( 84) covalent geometry : bond 0.00502 (20374) covalent geometry : angle 0.74151 (27699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 356 time to evaluate : 2.150 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7393 (p0) cc_final: 0.7086 (p0) REVERT: A 163 THR cc_start: 0.6430 (t) cc_final: 0.6213 (t) REVERT: B 542 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8133 (ttp80) REVERT: B 602 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8264 (pp) REVERT: D 68 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7976 (tttp) REVERT: D 105 THR cc_start: 0.8076 (m) cc_final: 0.7400 (p) REVERT: E 33 ASN cc_start: 0.7650 (p0) cc_final: 0.7358 (p0) REVERT: E 164 GLU cc_start: 0.7306 (pm20) cc_final: 0.7061 (pt0) REVERT: E 317 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8421 (t80) REVERT: E 475 MET cc_start: 0.8266 (mmm) cc_final: 0.7071 (ptp) REVERT: F 622 ILE cc_start: 0.7475 (tp) cc_final: 0.6890 (tt) REVERT: F 634 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7930 (mt-10) REVERT: F 661 LEU cc_start: 0.8106 (tt) cc_final: 0.7714 (tt) REVERT: H 48 MET cc_start: 0.7292 (mmm) cc_final: 0.6997 (mmm) REVERT: I 77 ILE cc_start: 0.8983 (pt) cc_final: 0.8704 (mm) REVERT: I 105 THR cc_start: 0.8637 (m) cc_final: 0.8083 (p) REVERT: K 121 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7771 (ttmm) REVERT: K 217 TYR cc_start: 0.8044 (m-80) cc_final: 0.7562 (m-80) REVERT: M 4 LEU cc_start: 0.8892 (mp) cc_final: 0.8663 (mp) REVERT: N 55 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8792 (mtpp) REVERT: N 68 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7843 (mtpp) REVERT: N 105 THR cc_start: 0.8341 (m) cc_final: 0.7782 (p) outliers start: 103 outliers final: 83 residues processed: 415 average time/residue: 0.2957 time to fit residues: 191.4573 Evaluate side-chains 429 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 344 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 195 ASN E 374 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN L 640 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097250 restraints weight = 37377.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096887 restraints weight = 29517.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097322 restraints weight = 31867.800| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20481 Z= 0.162 Angle : 0.733 11.335 27978 Z= 0.354 Chirality : 0.046 0.278 3301 Planarity : 0.004 0.041 3441 Dihedral : 7.980 64.542 3941 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 4.22 % Allowed : 21.71 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2442 helix: -0.16 (0.27), residues: 411 sheet: -0.68 (0.20), residues: 729 loop : -1.07 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP M 101 HIS 0.004 0.001 HIS K 374 PHE 0.012 0.001 PHE K 317 TYR 0.014 0.001 TYR E 361 ARG 0.009 0.001 ARG I 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 12) link_NAG-ASN : angle 2.04446 ( 36) link_ALPHA1-6 : bond 0.00445 ( 8) link_ALPHA1-6 : angle 2.03679 ( 24) link_BETA1-4 : bond 0.00614 ( 24) link_BETA1-4 : angle 1.98801 ( 72) link_ALPHA1-2 : bond 0.00359 ( 9) link_ALPHA1-2 : angle 3.11048 ( 27) link_ALPHA1-3 : bond 0.01105 ( 12) link_ALPHA1-3 : angle 1.26087 ( 36) hydrogen bonds : bond 0.03388 ( 518) hydrogen bonds : angle 5.14489 ( 1353) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.45613 ( 84) covalent geometry : bond 0.00378 (20374) covalent geometry : angle 0.71100 (27699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 364 time to evaluate : 2.108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7385 (p0) cc_final: 0.7104 (p0) REVERT: B 542 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8036 (ttp80) REVERT: B 602 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8250 (pp) REVERT: C 10 GLU cc_start: 0.8401 (tp30) cc_final: 0.7784 (mm-30) REVERT: C 12 LYS cc_start: 0.7209 (mttt) cc_final: 0.6835 (mttt) REVERT: D 68 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8089 (tttp) REVERT: D 105 THR cc_start: 0.8426 (m) cc_final: 0.7810 (p) REVERT: E 33 ASN cc_start: 0.7711 (p0) cc_final: 0.7416 (p0) REVERT: E 164 GLU cc_start: 0.7297 (pm20) cc_final: 0.7069 (pt0) REVERT: E 317 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8251 (t80) REVERT: E 475 MET cc_start: 0.8268 (mmm) cc_final: 0.7070 (ptp) REVERT: F 622 ILE cc_start: 0.7194 (tp) cc_final: 0.6925 (tp) REVERT: F 650 GLN cc_start: 0.8952 (tp40) cc_final: 0.8090 (tm-30) REVERT: F 661 LEU cc_start: 0.8162 (tt) cc_final: 0.7727 (tt) REVERT: H 48 MET cc_start: 0.7288 (mmm) cc_final: 0.7003 (mmm) REVERT: I 105 THR cc_start: 0.8725 (m) cc_final: 0.8193 (p) REVERT: K 121 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7543 (ttmm) REVERT: K 217 TYR cc_start: 0.8034 (m-80) cc_final: 0.7492 (m-80) REVERT: K 268 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8376 (mmmm) REVERT: K 340 ASP cc_start: 0.7694 (m-30) cc_final: 0.7490 (t0) REVERT: N 55 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8824 (mtpp) REVERT: N 64 PHE cc_start: 0.7598 (m-80) cc_final: 0.7370 (m-80) REVERT: N 68 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7875 (mtpp) REVERT: N 105 THR cc_start: 0.8303 (m) cc_final: 0.7834 (p) outliers start: 90 outliers final: 76 residues processed: 414 average time/residue: 0.3012 time to fit residues: 193.7565 Evaluate side-chains 429 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 166 optimal weight: 0.0170 chunk 150 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098119 restraints weight = 37723.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097592 restraints weight = 30490.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098172 restraints weight = 31804.282| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20481 Z= 0.144 Angle : 0.732 11.933 27978 Z= 0.352 Chirality : 0.046 0.275 3301 Planarity : 0.004 0.040 3441 Dihedral : 7.670 62.241 3941 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.87 % Favored : 94.88 % Rotamer: Outliers : 3.47 % Allowed : 22.64 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2442 helix: -0.09 (0.27), residues: 411 sheet: -0.59 (0.20), residues: 738 loop : -1.03 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 101 HIS 0.004 0.001 HIS K 374 PHE 0.026 0.001 PHE F 522 TYR 0.014 0.001 TYR E 361 ARG 0.009 0.001 ARG N 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 12) link_NAG-ASN : angle 1.99943 ( 36) link_ALPHA1-6 : bond 0.00494 ( 8) link_ALPHA1-6 : angle 2.00307 ( 24) link_BETA1-4 : bond 0.00609 ( 24) link_BETA1-4 : angle 1.89663 ( 72) link_ALPHA1-2 : bond 0.00387 ( 9) link_ALPHA1-2 : angle 3.10643 ( 27) link_ALPHA1-3 : bond 0.01123 ( 12) link_ALPHA1-3 : angle 1.23528 ( 36) hydrogen bonds : bond 0.03275 ( 518) hydrogen bonds : angle 5.06169 ( 1353) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.06813 ( 84) covalent geometry : bond 0.00334 (20374) covalent geometry : angle 0.71325 (27699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 2.370 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7370 (p0) cc_final: 0.7111 (p0) REVERT: B 542 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.8096 (ttp80) REVERT: B 602 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8228 (pp) REVERT: D 55 LYS cc_start: 0.8474 (mmmt) cc_final: 0.7915 (mttt) REVERT: D 68 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8061 (tttp) REVERT: E 33 ASN cc_start: 0.7697 (p0) cc_final: 0.7439 (p0) REVERT: E 164 GLU cc_start: 0.7325 (pm20) cc_final: 0.7097 (pt0) REVERT: E 475 MET cc_start: 0.8218 (mmm) cc_final: 0.7078 (ptp) REVERT: F 622 ILE cc_start: 0.7071 (tp) cc_final: 0.6637 (tt) REVERT: F 633 LYS cc_start: 0.8870 (pptt) cc_final: 0.8373 (ptpp) REVERT: F 650 GLN cc_start: 0.8918 (tp40) cc_final: 0.7535 (tm-30) REVERT: F 661 LEU cc_start: 0.8149 (tt) cc_final: 0.7898 (tt) REVERT: I 55 LYS cc_start: 0.8522 (mmmt) cc_final: 0.7870 (mttt) REVERT: I 105 THR cc_start: 0.8485 (m) cc_final: 0.7936 (p) REVERT: K 121 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7726 (ttmm) REVERT: K 217 TYR cc_start: 0.8016 (m-80) cc_final: 0.7450 (m-80) REVERT: K 268 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8394 (mmmm) REVERT: K 426 MET cc_start: 0.6435 (pmm) cc_final: 0.5836 (ptt) REVERT: M 70 MET cc_start: 0.8720 (mpp) cc_final: 0.8260 (mpt) REVERT: N 55 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8821 (mtpp) REVERT: N 68 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7843 (mtpp) REVERT: N 105 THR cc_start: 0.8370 (m) cc_final: 0.7839 (p) outliers start: 74 outliers final: 61 residues processed: 396 average time/residue: 0.2888 time to fit residues: 178.6117 Evaluate side-chains 411 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 349 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 181 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 216 optimal weight: 0.0570 chunk 177 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS E 374 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.131915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100921 restraints weight = 37717.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100592 restraints weight = 29609.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101541 restraints weight = 34782.677| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20481 Z= 0.118 Angle : 0.713 11.852 27978 Z= 0.342 Chirality : 0.045 0.274 3301 Planarity : 0.004 0.040 3441 Dihedral : 7.094 57.873 3941 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.55 % Favored : 95.21 % Rotamer: Outliers : 2.44 % Allowed : 23.53 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.18), residues: 2442 helix: 0.04 (0.27), residues: 402 sheet: -0.26 (0.20), residues: 720 loop : -0.91 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 101 HIS 0.007 0.001 HIS K 374 PHE 0.008 0.001 PHE M 64 TYR 0.016 0.001 TYR N 89 ARG 0.008 0.001 ARG H 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 12) link_NAG-ASN : angle 1.88090 ( 36) link_ALPHA1-6 : bond 0.00682 ( 8) link_ALPHA1-6 : angle 1.90482 ( 24) link_BETA1-4 : bond 0.00577 ( 24) link_BETA1-4 : angle 1.67542 ( 72) link_ALPHA1-2 : bond 0.00444 ( 9) link_ALPHA1-2 : angle 3.10357 ( 27) link_ALPHA1-3 : bond 0.01150 ( 12) link_ALPHA1-3 : angle 1.15602 ( 36) hydrogen bonds : bond 0.03003 ( 518) hydrogen bonds : angle 4.90864 ( 1353) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.19769 ( 84) covalent geometry : bond 0.00262 (20374) covalent geometry : angle 0.69471 (27699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6012.36 seconds wall clock time: 106 minutes 33.47 seconds (6393.47 seconds total)