Starting phenix.real_space_refine on Sun Aug 24 12:16:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8saz_40285/08_2025/8saz_40285_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8saz_40285/08_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_40285/08_2025/8saz_40285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8saz_40285/08_2025/8saz_40285.map" model { file = "/net/cci-nas-00/data/ceres_data/8saz_40285/08_2025/8saz_40285_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8saz_40285/08_2025/8saz_40285_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.64, per 1000 atoms: 0.23 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: 1.82 Conformation dependent library (CDL) restraints added in 917.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.75 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: 3.06 Time building geometry restraints manager: 2.43 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: 0.500 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- 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 : 2.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (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 ARG 0.012 0.001 ARG A 166 TYR 0.045 0.002 TYR M 116 PHE 0.034 0.002 PHE I 64 TRP 0.035 0.002 TRP A 427 HIS 0.008 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00599 (20374) covalent geometry : angle 0.97879 (27699) SS BOND : bond 0.00533 ( 42) SS BOND : angle 1.66382 ( 84) hydrogen bonds : bond 0.24209 ( 518) hydrogen bonds : angle 9.64635 ( 1353) 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) 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_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 3.27868 ( 36) *********************** 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 : 0.662 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 78 ASP cc_start: 0.7800 (t0) cc_final: 0.7600 (p0) 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: 0.7165 (m-80) REVERT: B 607 ASN cc_start: 0.8372 (p0) cc_final: 0.8163 (p0) REVERT: B 659 ASP cc_start: 0.8091 (m-30) cc_final: 0.7823 (m-30) REVERT: C 91 THR cc_start: 0.8163 (m) cc_final: 0.7948 (t) REVERT: D 25 THR cc_start: 0.8366 (t) cc_final: 0.8122 (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: 0.7386 (t0) REVERT: D 89 TYR cc_start: 0.8125 (m-80) cc_final: 0.7532 (m-80) REVERT: E 104 MET cc_start: 0.9010 (ttt) cc_final: 0.8792 (ttp) REVERT: E 121 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7249 (ttmm) REVERT: E 217 TYR cc_start: 0.7678 (m-80) cc_final: 0.7425 (m-80) REVERT: F 534 SER cc_start: 0.9393 (t) cc_final: 0.9146 (p) REVERT: F 602 LEU cc_start: 0.8622 (pt) cc_final: 0.8339 (pp) REVERT: F 610 TRP cc_start: 0.8454 (t-100) cc_final: 0.8079 (t-100) REVERT: H 101 TRP cc_start: 0.8527 (t60) cc_final: 0.8319 (t-100) REVERT: I 35 VAL cc_start: 0.9046 (t) cc_final: 0.8833 (p) REVERT: I 77 ILE cc_start: 0.8766 (mt) cc_final: 0.8423 (mt) REVERT: I 89 TYR cc_start: 0.8214 (m-80) cc_final: 0.7432 (m-80) REVERT: K 121 LYS cc_start: 0.7643 (ptpt) cc_final: 0.7295 (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: 0.6194 (tt) REVERT: L 631 TRP cc_start: 0.8854 (t-100) cc_final: 0.8566 (t-100) REVERT: L 659 ASP cc_start: 0.7798 (m-30) cc_final: 0.7569 (m-30) REVERT: M 4 LEU cc_start: 0.8512 (mm) cc_final: 0.8234 (mp) REVERT: N 25 THR cc_start: 0.8504 (t) cc_final: 0.8128 (p) REVERT: N 89 TYR cc_start: 0.8135 (m-80) cc_final: 0.7848 (m-80) outliers start: 3 outliers final: 0 residues processed: 745 average time/residue: 0.1481 time to fit residues: 165.8543 Evaluate side-chains 424 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- 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 302 ASN E 328 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102106 restraints weight = 37204.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101699 restraints weight = 32439.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102623 restraints weight = 36740.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103540 restraints weight = 26616.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103784 restraints weight = 24135.459| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3292 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= 0.219 Angle : 0.841 10.259 27978 Z= 0.411 Chirality : 0.050 0.296 3301 Planarity : 0.005 0.060 3441 Dihedral : 12.754 88.471 3941 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 3.42 % Allowed : 14.11 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.17), residues: 2442 helix: -1.24 (0.24), residues: 429 sheet: -1.40 (0.19), residues: 690 loop : -1.04 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 59 TYR 0.024 0.002 TYR M 27 PHE 0.028 0.003 PHE K 233 TRP 0.015 0.002 TRP A 427 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00511 (20374) covalent geometry : angle 0.81024 (27699) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.60708 ( 84) hydrogen bonds : bond 0.04644 ( 518) hydrogen bonds : angle 6.46955 ( 1353) link_ALPHA1-2 : bond 0.00415 ( 9) link_ALPHA1-2 : angle 3.08842 ( 27) link_ALPHA1-3 : bond 0.01158 ( 12) link_ALPHA1-3 : angle 1.71114 ( 36) link_ALPHA1-6 : bond 0.00375 ( 8) link_ALPHA1-6 : angle 2.12309 ( 24) link_BETA1-4 : bond 0.00911 ( 24) link_BETA1-4 : angle 3.13336 ( 72) link_NAG-ASN : bond 0.00520 ( 12) link_NAG-ASN : angle 2.30101 ( 36) *********************** 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 501 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 428 time to evaluate : 0.764 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 97 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8195 (ptpp) REVERT: A 114 GLN cc_start: 0.8565 (tp40) cc_final: 0.8170 (tp40) REVERT: A 121 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7427 (ttmm) REVERT: C 11 VAL cc_start: 0.8479 (t) cc_final: 0.8207 (m) REVERT: D 87 ASP cc_start: 0.7462 (t0) cc_final: 0.7180 (t0) REVERT: D 89 TYR cc_start: 0.7693 (m-80) cc_final: 0.7361 (m-80) REVERT: E 33 ASN cc_start: 0.7350 (p0) cc_final: 0.7016 (p0) REVERT: E 104 MET cc_start: 0.9100 (ttt) cc_final: 0.8771 (ttp) REVERT: E 121 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7424 (ttmm) REVERT: E 217 TYR cc_start: 0.8116 (m-80) cc_final: 0.7806 (m-80) REVERT: E 475 MET cc_start: 0.8405 (mmm) cc_final: 0.7110 (ptp) REVERT: F 534 SER cc_start: 0.9320 (t) cc_final: 0.9117 (p) REVERT: F 602 LEU cc_start: 0.8617 (pt) cc_final: 0.8414 (pp) REVERT: F 646 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9136 (mm) REVERT: H 4 LEU cc_start: 0.8950 (mt) cc_final: 0.8702 (mp) REVERT: H 101 TRP cc_start: 0.8715 (t60) cc_final: 0.8454 (t-100) REVERT: I 56 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7676 (mtt90) REVERT: K 121 LYS cc_start: 0.7815 (ptpt) cc_final: 0.7587 (ttmm) REVERT: K 268 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7896 (mmmm) REVERT: K 426 MET cc_start: 0.6914 (pmm) cc_final: 0.6026 (pmm) REVERT: L 542 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.8163 (mtp-110) REVERT: L 595 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8810 (mt) REVERT: L 622 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7202 (tt) REVERT: M 12 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7707 (mmtp) REVERT: N 85 GLU cc_start: 0.7101 (pt0) cc_final: 0.6803 (pt0) outliers start: 73 outliers final: 47 residues processed: 477 average time/residue: 0.1429 time to fit residues: 103.9524 Evaluate side-chains 414 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 181 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 602 LEU 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 150 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 295 VAL 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 390 LEU Chi-restraints excluded: chain E residue 443 ILE 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 I residue 48 LEU Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 92 SER 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 265 LEU Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 620 SER Chi-restraints excluded: chain L residue 622 ILE 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 227 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 238 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 188 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: D 71 ASN E 343 GLN H 62 GLN I 16 GLN L 658 GLN M 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098393 restraints weight = 37654.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097725 restraints weight = 34700.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098462 restraints weight = 35905.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099434 restraints weight = 28616.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099674 restraints weight = 25511.880| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20481 Z= 0.225 Angle : 0.791 10.272 27978 Z= 0.386 Chirality : 0.049 0.316 3301 Planarity : 0.005 0.050 3441 Dihedral : 10.514 81.793 3941 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 4.45 % Allowed : 16.46 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.17), residues: 2442 helix: -0.75 (0.26), residues: 414 sheet: -1.05 (0.19), residues: 726 loop : -1.10 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 98 TYR 0.018 0.002 TYR K 40 PHE 0.016 0.002 PHE A 317 TRP 0.027 0.002 TRP M 101 HIS 0.006 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00526 (20374) covalent geometry : angle 0.76284 (27699) SS BOND : bond 0.00326 ( 42) SS BOND : angle 1.56155 ( 84) hydrogen bonds : bond 0.04193 ( 518) hydrogen bonds : angle 5.86846 ( 1353) link_ALPHA1-2 : bond 0.00271 ( 9) link_ALPHA1-2 : angle 3.29713 ( 27) link_ALPHA1-3 : bond 0.01202 ( 12) link_ALPHA1-3 : angle 1.62824 ( 36) link_ALPHA1-6 : bond 0.00366 ( 8) link_ALPHA1-6 : angle 2.08306 ( 24) link_BETA1-4 : bond 0.00808 ( 24) link_BETA1-4 : angle 2.58760 ( 72) link_NAG-ASN : bond 0.00534 ( 12) link_NAG-ASN : angle 2.30972 ( 36) *********************** 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 497 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 402 time to evaluate : 0.668 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 97 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8272 (ptpp) REVERT: B 653 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8666 (tm-30) REVERT: B 660 LEU cc_start: 0.8245 (tp) cc_final: 0.7929 (tp) REVERT: D 71 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8049 (t0) REVERT: E 33 ASN cc_start: 0.7450 (p0) cc_final: 0.7173 (p0) REVERT: E 103 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7455 (mm110) REVERT: E 217 TYR cc_start: 0.8214 (m-80) cc_final: 0.7914 (m-80) REVERT: E 475 MET cc_start: 0.8480 (mmm) cc_final: 0.7150 (ptp) REVERT: F 602 LEU cc_start: 0.8943 (pt) cc_final: 0.8674 (pp) REVERT: F 646 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8999 (mm) REVERT: H 80 TYR cc_start: 0.7989 (m-10) cc_final: 0.7366 (m-10) REVERT: H 101 TRP cc_start: 0.8812 (t60) cc_final: 0.8426 (t-100) REVERT: I 87 ASP cc_start: 0.7262 (t0) cc_final: 0.7060 (t0) REVERT: K 121 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7563 (ttmm) REVERT: K 217 TYR cc_start: 0.8092 (m-80) cc_final: 0.7457 (m-80) REVERT: L 542 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.8281 (mtp-110) REVERT: L 648 GLU cc_start: 0.8186 (pp20) cc_final: 0.7780 (tp30) REVERT: M 12 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7707 (mmtp) REVERT: M 111 TYR cc_start: 0.9082 (m-80) cc_final: 0.8807 (m-80) REVERT: N 23 THR cc_start: 0.8422 (m) cc_final: 0.8206 (m) REVERT: N 105 THR cc_start: 0.8188 (m) cc_final: 0.7640 (p) outliers start: 95 outliers final: 66 residues processed: 460 average time/residue: 0.1271 time to fit residues: 90.4288 Evaluate side-chains 428 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 360 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 181 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 475 MET 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 615 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 245 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 390 LEU 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 627 THR 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 56 ARG Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 123 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 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 390 LEU 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 L residue 661 LEU 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 75 SER Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 36 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 44 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 152 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 16 GLN D 71 ASN E 389 ASN K 33 ASN K 389 ASN L 640 GLN L 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099406 restraints weight = 37515.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098539 restraints weight = 33307.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099500 restraints weight = 38844.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100309 restraints weight = 27704.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100586 restraints weight = 25332.859| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 20481 Z= 0.159 Angle : 0.741 12.916 27978 Z= 0.360 Chirality : 0.047 0.309 3301 Planarity : 0.004 0.046 3441 Dihedral : 9.400 76.971 3941 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 4.27 % Allowed : 18.14 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.17), residues: 2442 helix: -0.49 (0.26), residues: 414 sheet: -0.83 (0.20), residues: 702 loop : -1.13 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 504 TYR 0.016 0.002 TYR M 27 PHE 0.013 0.001 PHE A 317 TRP 0.026 0.001 TRP M 101 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00370 (20374) covalent geometry : angle 0.71030 (27699) SS BOND : bond 0.00287 ( 42) SS BOND : angle 2.12255 ( 84) hydrogen bonds : bond 0.03518 ( 518) hydrogen bonds : angle 5.54835 ( 1353) link_ALPHA1-2 : bond 0.00337 ( 9) link_ALPHA1-2 : angle 3.13597 ( 27) link_ALPHA1-3 : bond 0.01163 ( 12) link_ALPHA1-3 : angle 1.45188 ( 36) link_ALPHA1-6 : bond 0.00275 ( 8) link_ALPHA1-6 : angle 2.09896 ( 24) link_BETA1-4 : bond 0.00671 ( 24) link_BETA1-4 : angle 2.32958 ( 72) link_NAG-ASN : bond 0.00391 ( 12) link_NAG-ASN : angle 2.16138 ( 36) *********************** 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 484 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 393 time to evaluate : 0.506 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 97 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8235 (ptpp) REVERT: B 535 MET cc_start: 0.7377 (mpp) cc_final: 0.7137 (mpp) REVERT: B 653 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8650 (tm-30) REVERT: D 71 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8311 (t0) REVERT: E 33 ASN cc_start: 0.7431 (p0) cc_final: 0.7083 (p0) REVERT: E 475 MET cc_start: 0.8373 (mmm) cc_final: 0.7098 (ptp) REVERT: F 602 LEU cc_start: 0.8808 (pt) cc_final: 0.8591 (pp) REVERT: F 646 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8990 (mm) REVERT: H 101 TRP cc_start: 0.8828 (t60) cc_final: 0.8446 (t-100) REVERT: K 121 LYS cc_start: 0.7904 (ptpt) cc_final: 0.7427 (ttmm) REVERT: K 217 TYR cc_start: 0.8103 (m-80) cc_final: 0.7438 (m-80) REVERT: K 268 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8046 (mmmm) REVERT: K 502 LYS cc_start: 0.7453 (tptp) cc_final: 0.6994 (tptp) REVERT: L 542 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8259 (mtp-110) REVERT: L 595 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8766 (mt) REVERT: L 648 GLU cc_start: 0.8096 (pp20) cc_final: 0.7750 (tp30) REVERT: N 55 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8287 (mtpp) REVERT: N 68 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8112 (mtpt) REVERT: N 105 THR cc_start: 0.8013 (m) cc_final: 0.7464 (p) outliers start: 91 outliers final: 56 residues processed: 449 average time/residue: 0.1219 time to fit residues: 86.4009 Evaluate side-chains 420 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE 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 345 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 501 CYS 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 615 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 77 THR 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 152 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 213 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 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 604 CYS 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 64 PHE Chi-restraints excluded: chain I residue 91 CYS 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 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 345 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 535 MET Chi-restraints excluded: chain L residue 587 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 602 LEU 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 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 155 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 226 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN B 575 GLN B 658 GLN D 71 ASN F 577 GLN F 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100784 restraints weight = 37279.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100200 restraints weight = 33100.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101434 restraints weight = 37244.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101919 restraints weight = 26672.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102221 restraints weight = 24946.956| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20481 Z= 0.129 Angle : 0.719 11.380 27978 Z= 0.349 Chirality : 0.046 0.305 3301 Planarity : 0.004 0.043 3441 Dihedral : 8.614 71.099 3941 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 3.98 % Allowed : 19.69 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.17), residues: 2442 helix: -0.36 (0.27), residues: 411 sheet: -0.64 (0.20), residues: 702 loop : -1.11 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 63 TYR 0.017 0.001 TYR M 27 PHE 0.010 0.001 PHE A 317 TRP 0.025 0.001 TRP M 101 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00294 (20374) covalent geometry : angle 0.69068 (27699) SS BOND : bond 0.00266 ( 42) SS BOND : angle 2.09640 ( 84) hydrogen bonds : bond 0.03205 ( 518) hydrogen bonds : angle 5.32032 ( 1353) link_ALPHA1-2 : bond 0.00409 ( 9) link_ALPHA1-2 : angle 3.13181 ( 27) link_ALPHA1-3 : bond 0.01206 ( 12) link_ALPHA1-3 : angle 1.33489 ( 36) link_ALPHA1-6 : bond 0.00401 ( 8) link_ALPHA1-6 : angle 2.04088 ( 24) link_BETA1-4 : bond 0.00642 ( 24) link_BETA1-4 : angle 2.03597 ( 72) link_NAG-ASN : bond 0.00304 ( 12) link_NAG-ASN : angle 2.00807 ( 36) *********************** 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 478 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 393 time to evaluate : 0.818 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: B 535 MET cc_start: 0.7363 (mpp) cc_final: 0.7062 (mpp) REVERT: B 633 LYS cc_start: 0.8842 (pptt) cc_final: 0.8364 (ptpp) REVERT: D 71 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8378 (t0) REVERT: D 105 THR cc_start: 0.8070 (m) cc_final: 0.7455 (p) REVERT: E 33 ASN cc_start: 0.7581 (p0) cc_final: 0.7238 (p0) REVERT: E 475 MET cc_start: 0.8343 (mmm) cc_final: 0.6986 (ptp) REVERT: F 602 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8500 (pp) REVERT: F 646 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9001 (mm) REVERT: H 101 TRP cc_start: 0.8836 (t60) cc_final: 0.8457 (t-100) REVERT: K 121 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7452 (ttmm) REVERT: K 217 TYR cc_start: 0.8082 (m-80) cc_final: 0.7425 (m-80) REVERT: K 268 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8182 (mmmm) REVERT: L 595 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8655 (mt) REVERT: L 605 CYS cc_start: 0.4835 (p) cc_final: 0.3995 (p) REVERT: L 648 GLU cc_start: 0.8034 (pp20) cc_final: 0.7800 (tp30) REVERT: M 70 MET cc_start: 0.8755 (mpp) cc_final: 0.8054 (mpt) REVERT: N 55 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8494 (mtpp) REVERT: N 105 THR cc_start: 0.7984 (m) cc_final: 0.7502 (p) outliers start: 85 outliers final: 58 residues processed: 441 average time/residue: 0.1488 time to fit residues: 102.0576 Evaluate side-chains 426 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 201 CYS 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 481 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 54 CYS 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 201 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 45 LEU 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 54 CYS 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 390 LEU Chi-restraints excluded: chain L residue 595 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 645 LEU 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 81 MET Chi-restraints excluded: chain N residue 36 SER 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 115 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 117 optimal weight: 50.0000 chunk 198 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN B 591 GLN B 640 GLN D 71 ASN E 195 ASN F 575 GLN L 575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098607 restraints weight = 37491.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097743 restraints weight = 34008.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098605 restraints weight = 42101.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099527 restraints weight = 28731.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099794 restraints weight = 25862.375| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20481 Z= 0.168 Angle : 0.724 11.590 27978 Z= 0.348 Chirality : 0.046 0.295 3301 Planarity : 0.004 0.043 3441 Dihedral : 8.357 69.330 3941 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.75 % Favored : 95.00 % Rotamer: Outliers : 4.74 % Allowed : 19.41 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2442 helix: -0.24 (0.27), residues: 411 sheet: -0.57 (0.20), residues: 702 loop : -1.13 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 63 TYR 0.016 0.002 TYR C 33 PHE 0.018 0.002 PHE M 64 TRP 0.026 0.001 TRP M 101 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00394 (20374) covalent geometry : angle 0.69986 (27699) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.59039 ( 84) hydrogen bonds : bond 0.03316 ( 518) hydrogen bonds : angle 5.18943 ( 1353) link_ALPHA1-2 : bond 0.00353 ( 9) link_ALPHA1-2 : angle 3.08649 ( 27) link_ALPHA1-3 : bond 0.01161 ( 12) link_ALPHA1-3 : angle 1.34365 ( 36) link_ALPHA1-6 : bond 0.00297 ( 8) link_ALPHA1-6 : angle 2.04609 ( 24) link_BETA1-4 : bond 0.00647 ( 24) link_BETA1-4 : angle 2.09262 ( 72) link_NAG-ASN : bond 0.00441 ( 12) link_NAG-ASN : angle 2.13396 ( 36) *********************** 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: 101 poor density : 366 time to evaluate : 0.815 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: 0.7156 (p0) cc_final: 0.6651 (p0) REVERT: A 164 GLU cc_start: 0.7484 (pm20) cc_final: 0.6997 (pm20) REVERT: B 535 MET cc_start: 0.7492 (mpp) cc_final: 0.7098 (mpp) REVERT: D 71 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8450 (t0) REVERT: D 87 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7357 (t0) REVERT: D 105 THR cc_start: 0.8082 (m) cc_final: 0.7410 (p) REVERT: E 33 ASN cc_start: 0.7651 (p0) cc_final: 0.7326 (p0) REVERT: E 475 MET cc_start: 0.8367 (mmm) cc_final: 0.7009 (ptp) REVERT: F 646 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8979 (mm) REVERT: F 661 LEU cc_start: 0.8184 (tt) cc_final: 0.7956 (tt) REVERT: H 43 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6181 (mt0) REVERT: I 105 THR cc_start: 0.8521 (m) cc_final: 0.8034 (p) REVERT: K 121 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7761 (ttmm) REVERT: K 217 TYR cc_start: 0.8149 (m-80) cc_final: 0.7574 (m-80) REVERT: N 55 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8585 (mtpp) REVERT: N 105 THR cc_start: 0.8135 (m) cc_final: 0.7549 (p) outliers start: 101 outliers final: 75 residues processed: 431 average time/residue: 0.1455 time to fit residues: 98.6709 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 : 0.784 ------------------------------------------------------------------------------- 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 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 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 ILE 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 627 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 54 CYS 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 201 CYS 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 364 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 121 THR 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 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 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 345 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 501 CYS 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 645 LEU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 36 SER 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 46 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 230 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 591 GLN B 658 GLN D 71 ASN E 195 ASN F 640 GLN F 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098990 restraints weight = 37681.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097542 restraints weight = 35644.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098943 restraints weight = 42095.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099677 restraints weight = 28236.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100316 restraints weight = 26388.795| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20481 Z= 0.162 Angle : 0.728 11.397 27978 Z= 0.351 Chirality : 0.046 0.290 3301 Planarity : 0.004 0.042 3441 Dihedral : 8.127 64.386 3941 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 4.92 % Allowed : 19.22 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.17), residues: 2442 helix: -0.20 (0.27), residues: 411 sheet: -0.58 (0.20), residues: 711 loop : -1.10 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 85 TYR 0.015 0.001 TYR C 33 PHE 0.013 0.002 PHE M 64 TRP 0.023 0.001 TRP A 35 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00382 (20374) covalent geometry : angle 0.70014 (27699) SS BOND : bond 0.00369 ( 42) SS BOND : angle 2.06089 ( 84) hydrogen bonds : bond 0.03293 ( 518) hydrogen bonds : angle 5.16745 ( 1353) link_ALPHA1-2 : bond 0.00371 ( 9) link_ALPHA1-2 : angle 3.08873 ( 27) link_ALPHA1-3 : bond 0.01137 ( 12) link_ALPHA1-3 : angle 1.31573 ( 36) link_ALPHA1-6 : bond 0.00479 ( 8) link_ALPHA1-6 : angle 2.04017 ( 24) link_BETA1-4 : bond 0.00626 ( 24) link_BETA1-4 : angle 2.02024 ( 72) link_NAG-ASN : bond 0.00364 ( 12) link_NAG-ASN : angle 2.10355 ( 36) *********************** 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 474 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 369 time to evaluate : 0.824 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: 0.7101 (p0) cc_final: 0.6619 (p0) REVERT: A 164 GLU cc_start: 0.7484 (pm20) cc_final: 0.7277 (pt0) REVERT: B 535 MET cc_start: 0.7603 (mpp) cc_final: 0.7203 (mpp) REVERT: B 633 LYS cc_start: 0.8827 (pptt) cc_final: 0.8391 (ptpp) REVERT: D 87 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7242 (t0) REVERT: D 105 THR cc_start: 0.8026 (m) cc_final: 0.7381 (p) REVERT: E 33 ASN cc_start: 0.7645 (p0) cc_final: 0.7244 (p0) REVERT: E 475 MET cc_start: 0.8306 (mmm) cc_final: 0.7046 (ptp) REVERT: F 633 LYS cc_start: 0.8868 (pptt) cc_final: 0.8618 (ptpp) REVERT: F 646 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9057 (mm) REVERT: F 650 GLN cc_start: 0.9057 (tp40) cc_final: 0.8177 (tm-30) REVERT: F 661 LEU cc_start: 0.8103 (tt) cc_final: 0.7811 (tt) REVERT: H 10 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: H 43 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6479 (mt0) REVERT: I 105 THR cc_start: 0.8623 (m) cc_final: 0.8134 (p) REVERT: K 121 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7723 (ttmm) REVERT: K 164 GLU cc_start: 0.7224 (pm20) cc_final: 0.6916 (pt0) REVERT: K 217 TYR cc_start: 0.8124 (m-80) cc_final: 0.7534 (m-80) REVERT: N 23 THR cc_start: 0.8834 (p) cc_final: 0.8601 (p) REVERT: N 55 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8681 (mtpp) REVERT: N 68 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7920 (mtpt) REVERT: N 105 THR cc_start: 0.8144 (m) cc_final: 0.7642 (p) outliers start: 105 outliers final: 82 residues processed: 432 average time/residue: 0.1440 time to fit residues: 98.5508 Evaluate side-chains 441 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 356 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 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 645 LEU 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 35 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL 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 150 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 CYS 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 364 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 6 GLN 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 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 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 390 LEU Chi-restraints excluded: chain L residue 587 LEU 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 645 LEU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 105 TYR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 92 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 200 optimal weight: 0.0670 chunk 121 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 overall best weight: 2.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN H 62 GLN K 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099159 restraints weight = 37634.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098182 restraints weight = 33412.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099568 restraints weight = 30695.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099938 restraints weight = 24984.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100167 restraints weight = 24529.456| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20481 Z= 0.141 Angle : 0.712 11.644 27978 Z= 0.342 Chirality : 0.045 0.288 3301 Planarity : 0.004 0.041 3441 Dihedral : 7.822 61.067 3941 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.50 % Favored : 95.29 % Rotamer: Outliers : 4.17 % Allowed : 20.68 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.17), residues: 2442 helix: -0.18 (0.27), residues: 411 sheet: -0.53 (0.20), residues: 714 loop : -1.04 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 85 TYR 0.018 0.001 TYR E 361 PHE 0.013 0.001 PHE L 522 TRP 0.021 0.001 TRP A 35 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (20374) covalent geometry : angle 0.69007 (27699) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.34160 ( 84) hydrogen bonds : bond 0.03225 ( 518) hydrogen bonds : angle 5.07985 ( 1353) link_ALPHA1-2 : bond 0.00391 ( 9) link_ALPHA1-2 : angle 3.08052 ( 27) link_ALPHA1-3 : bond 0.01175 ( 12) link_ALPHA1-3 : angle 1.26725 ( 36) link_ALPHA1-6 : bond 0.00481 ( 8) link_ALPHA1-6 : angle 1.99798 ( 24) link_BETA1-4 : bond 0.00602 ( 24) link_BETA1-4 : angle 1.93431 ( 72) link_NAG-ASN : bond 0.00309 ( 12) link_NAG-ASN : angle 2.03092 ( 36) *********************** 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 451 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 362 time to evaluate : 0.834 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: 0.7270 (p0) cc_final: 0.6761 (p0) REVERT: B 535 MET cc_start: 0.7530 (mpp) cc_final: 0.7148 (mpp) REVERT: B 633 LYS cc_start: 0.8868 (pptt) cc_final: 0.8427 (ptpp) REVERT: D 68 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7981 (tttp) REVERT: D 105 THR cc_start: 0.7980 (m) cc_final: 0.7328 (p) REVERT: E 33 ASN cc_start: 0.7661 (p0) cc_final: 0.7299 (p0) REVERT: E 164 GLU cc_start: 0.7044 (pm20) cc_final: 0.6825 (pt0) REVERT: E 475 MET cc_start: 0.8242 (mmm) cc_final: 0.6950 (ptp) REVERT: F 622 ILE cc_start: 0.7280 (tp) cc_final: 0.6955 (tp) REVERT: F 633 LYS cc_start: 0.8921 (pptt) cc_final: 0.8594 (ptpp) REVERT: F 634 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7692 (mt-10) REVERT: F 646 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8987 (mm) REVERT: F 648 GLU cc_start: 0.7943 (pp20) cc_final: 0.7654 (tp30) REVERT: F 650 GLN cc_start: 0.9022 (tp40) cc_final: 0.8137 (tm-30) REVERT: F 661 LEU cc_start: 0.8103 (tt) cc_final: 0.7496 (mp) REVERT: H 10 GLU cc_start: 0.8325 (tp30) cc_final: 0.7917 (mm-30) REVERT: H 43 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6615 (mt0) REVERT: I 105 THR cc_start: 0.8616 (m) cc_final: 0.8080 (p) REVERT: K 121 LYS cc_start: 0.8052 (ptpt) cc_final: 0.7678 (ttmm) REVERT: K 164 GLU cc_start: 0.7153 (pm20) cc_final: 0.6861 (pt0) REVERT: K 217 TYR cc_start: 0.8093 (m-80) cc_final: 0.7486 (m-80) REVERT: M 70 MET cc_start: 0.8831 (mpp) cc_final: 0.8115 (mpt) REVERT: N 55 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8735 (mtpp) REVERT: N 105 THR cc_start: 0.8301 (m) cc_final: 0.7742 (p) outliers start: 89 outliers final: 73 residues processed: 420 average time/residue: 0.1436 time to fit residues: 95.3156 Evaluate side-chains 425 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 351 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 213 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 620 SER Chi-restraints excluded: chain B residue 645 LEU 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 35 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 100 MET 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 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 364 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 121 THR 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 K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL 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 390 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 105 TYR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 48 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 129 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 198 optimal weight: 30.0000 chunk 95 optimal weight: 0.2980 chunk 225 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS K 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099975 restraints weight = 37051.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099103 restraints weight = 33271.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100192 restraints weight = 38272.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100791 restraints weight = 27486.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101122 restraints weight = 25262.715| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20481 Z= 0.138 Angle : 0.714 12.371 27978 Z= 0.342 Chirality : 0.045 0.283 3301 Planarity : 0.004 0.040 3441 Dihedral : 7.452 57.121 3941 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.59 % Favored : 95.21 % Rotamer: Outliers : 3.70 % Allowed : 21.33 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 2442 helix: -0.12 (0.27), residues: 411 sheet: -0.35 (0.20), residues: 702 loop : -1.03 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 85 TYR 0.018 0.001 TYR K 361 PHE 0.011 0.001 PHE L 522 TRP 0.019 0.001 TRP A 35 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (20374) covalent geometry : angle 0.69237 (27699) SS BOND : bond 0.00337 ( 42) SS BOND : angle 1.50613 ( 84) hydrogen bonds : bond 0.03165 ( 518) hydrogen bonds : angle 5.02185 ( 1353) link_ALPHA1-2 : bond 0.00405 ( 9) link_ALPHA1-2 : angle 3.05975 ( 27) link_ALPHA1-3 : bond 0.01162 ( 12) link_ALPHA1-3 : angle 1.24287 ( 36) link_ALPHA1-6 : bond 0.00528 ( 8) link_ALPHA1-6 : angle 1.96209 ( 24) link_BETA1-4 : bond 0.00592 ( 24) link_BETA1-4 : angle 1.84969 ( 72) link_NAG-ASN : bond 0.00285 ( 12) link_NAG-ASN : angle 2.00003 ( 36) *********************** 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 443 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 364 time to evaluate : 0.862 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: 0.7159 (p0) cc_final: 0.6785 (p0) REVERT: B 654 GLU cc_start: 0.8892 (tp30) cc_final: 0.8585 (tp30) REVERT: D 68 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7967 (tttp) REVERT: D 105 THR cc_start: 0.8009 (m) cc_final: 0.7352 (p) REVERT: E 33 ASN cc_start: 0.7665 (p0) cc_final: 0.7327 (p0) REVERT: E 164 GLU cc_start: 0.7085 (pm20) cc_final: 0.6840 (pt0) REVERT: E 475 MET cc_start: 0.8226 (mmm) cc_final: 0.6993 (ptp) REVERT: F 622 ILE cc_start: 0.7272 (tp) cc_final: 0.6824 (tt) REVERT: F 633 LYS cc_start: 0.8911 (pptt) cc_final: 0.8556 (ptpp) REVERT: F 634 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7717 (mt-10) REVERT: F 646 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9017 (mm) REVERT: F 647 GLU cc_start: 0.7856 (tt0) cc_final: 0.7633 (tt0) REVERT: F 650 GLN cc_start: 0.8953 (tp40) cc_final: 0.8158 (tm-30) REVERT: F 661 LEU cc_start: 0.8072 (tt) cc_final: 0.7768 (tt) REVERT: H 10 GLU cc_start: 0.8458 (tp30) cc_final: 0.8055 (mm-30) REVERT: H 43 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6806 (mt0) REVERT: I 105 THR cc_start: 0.8547 (m) cc_final: 0.7973 (p) REVERT: K 121 LYS cc_start: 0.8091 (ptpt) cc_final: 0.7706 (ttmm) REVERT: K 164 GLU cc_start: 0.7172 (pm20) cc_final: 0.6851 (pm20) REVERT: K 217 TYR cc_start: 0.8040 (m-80) cc_final: 0.7427 (m-80) REVERT: N 55 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8737 (mtpp) REVERT: N 105 THR cc_start: 0.8243 (m) cc_final: 0.7813 (p) outliers start: 79 outliers final: 71 residues processed: 414 average time/residue: 0.1460 time to fit residues: 94.8791 Evaluate side-chains 420 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 348 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 100 MET 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 201 CYS 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 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 616 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 100 MET 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 245 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER 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 K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL 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 390 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 635 ILE Chi-restraints excluded: chain M residue 105 TYR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 90 CYS 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 16 optimal weight: 0.0030 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 640 GLN L 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099882 restraints weight = 37639.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098711 restraints weight = 34599.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099736 restraints weight = 43811.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100465 restraints weight = 29031.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100782 restraints weight = 26861.709| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20481 Z= 0.135 Angle : 0.718 12.346 27978 Z= 0.343 Chirality : 0.045 0.280 3301 Planarity : 0.004 0.040 3441 Dihedral : 7.232 56.813 3941 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.50 % Favored : 95.29 % Rotamer: Outliers : 3.70 % Allowed : 21.38 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.17), residues: 2442 helix: -0.05 (0.27), residues: 411 sheet: -0.32 (0.20), residues: 705 loop : -1.00 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 63 TYR 0.020 0.001 TYR K 361 PHE 0.012 0.001 PHE M 64 TRP 0.017 0.001 TRP A 35 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00317 (20374) covalent geometry : angle 0.69895 (27699) SS BOND : bond 0.00315 ( 42) SS BOND : angle 1.12237 ( 84) hydrogen bonds : bond 0.03054 ( 518) hydrogen bonds : angle 4.98327 ( 1353) link_ALPHA1-2 : bond 0.00420 ( 9) link_ALPHA1-2 : angle 3.05681 ( 27) link_ALPHA1-3 : bond 0.01138 ( 12) link_ALPHA1-3 : angle 1.22947 ( 36) link_ALPHA1-6 : bond 0.00577 ( 8) link_ALPHA1-6 : angle 1.94485 ( 24) link_BETA1-4 : bond 0.00588 ( 24) link_BETA1-4 : angle 1.80854 ( 72) link_NAG-ASN : bond 0.00267 ( 12) link_NAG-ASN : angle 1.98627 ( 36) ********************** 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 428 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 349 time to evaluate : 0.760 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: 0.7318 (p0) cc_final: 0.6972 (p0) REVERT: C 10 GLU cc_start: 0.8241 (tp30) cc_final: 0.7833 (mm-30) REVERT: D 68 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7995 (tttp) REVERT: D 105 THR cc_start: 0.8259 (m) cc_final: 0.7644 (p) REVERT: E 33 ASN cc_start: 0.7659 (p0) cc_final: 0.7369 (p0) REVERT: E 164 GLU cc_start: 0.7149 (pm20) cc_final: 0.6922 (pt0) REVERT: E 475 MET cc_start: 0.8216 (mmm) cc_final: 0.6989 (ptp) REVERT: F 622 ILE cc_start: 0.7246 (tp) cc_final: 0.6798 (tt) REVERT: F 633 LYS cc_start: 0.8903 (pptt) cc_final: 0.8664 (ptpp) REVERT: F 646 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8987 (mm) REVERT: F 650 GLN cc_start: 0.8901 (tp40) cc_final: 0.8216 (tm-30) REVERT: H 10 GLU cc_start: 0.8453 (tp30) cc_final: 0.8120 (mm-30) REVERT: I 105 THR cc_start: 0.8572 (m) cc_final: 0.8029 (p) REVERT: K 121 LYS cc_start: 0.8107 (ptpt) cc_final: 0.7696 (ttmm) REVERT: K 164 GLU cc_start: 0.7246 (pm20) cc_final: 0.6996 (pm20) REVERT: K 217 TYR cc_start: 0.8033 (m-80) cc_final: 0.7418 (m-80) REVERT: K 426 MET cc_start: 0.7142 (pmm) cc_final: 0.6923 (pmm) REVERT: L 648 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7818 (tp30) REVERT: N 55 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8742 (mtpp) REVERT: N 64 PHE cc_start: 0.7356 (m-80) cc_final: 0.7057 (m-80) REVERT: N 105 THR cc_start: 0.8326 (m) cc_final: 0.7802 (p) outliers start: 79 outliers final: 71 residues processed: 403 average time/residue: 0.1443 time to fit residues: 91.8542 Evaluate side-chains 416 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 344 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 100 MET 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 201 CYS 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 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL 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 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 364 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain I residue 22 CYS 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 K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL 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 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 390 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain M residue 105 TYR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 149 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 172 optimal weight: 0.1980 chunk 128 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098302 restraints weight = 37886.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098155 restraints weight = 29070.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098858 restraints weight = 33715.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099504 restraints weight = 24789.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100039 restraints weight = 22482.572| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20481 Z= 0.167 Angle : 0.734 12.324 27978 Z= 0.352 Chirality : 0.046 0.273 3301 Planarity : 0.004 0.041 3441 Dihedral : 7.234 57.411 3941 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.67 % Favored : 95.13 % Rotamer: Outliers : 3.66 % Allowed : 21.47 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.17), residues: 2442 helix: -0.04 (0.27), residues: 411 sheet: -0.40 (0.20), residues: 690 loop : -0.96 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 85 TYR 0.019 0.002 TYR A 361 PHE 0.012 0.001 PHE K 376 TRP 0.022 0.001 TRP B 628 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00394 (20374) covalent geometry : angle 0.71442 (27699) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.23664 ( 84) hydrogen bonds : bond 0.03267 ( 518) hydrogen bonds : angle 5.02525 ( 1353) link_ALPHA1-2 : bond 0.00375 ( 9) link_ALPHA1-2 : angle 3.07672 ( 27) link_ALPHA1-3 : bond 0.01054 ( 12) link_ALPHA1-3 : angle 1.26039 ( 36) link_ALPHA1-6 : bond 0.00537 ( 8) link_ALPHA1-6 : angle 1.94114 ( 24) link_BETA1-4 : bond 0.00611 ( 24) link_BETA1-4 : angle 1.89285 ( 72) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.07625 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.75 seconds wall clock time: 55 minutes 42.92 seconds (3342.92 seconds total)