Starting phenix.real_space_refine on Wed Mar 4 16:45:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sc5_25022/03_2026/7sc5_25022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sc5_25022/03_2026/7sc5_25022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sc5_25022/03_2026/7sc5_25022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sc5_25022/03_2026/7sc5_25022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sc5_25022/03_2026/7sc5_25022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sc5_25022/03_2026/7sc5_25022.map" } resolution = 3.88 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= 0.000 sd= 0.001 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 99 5.16 5 C 9192 2.51 5 N 2511 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "D" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "F" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 3.39, per 1000 atoms: 0.23 Number of scatterers: 14703 At special positions: 0 Unit cell: (122.57, 130.81, 129.78, 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 99 16.00 O 2901 8.00 N 2511 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 443 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 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 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.02 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 443 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=3, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 152 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 331 " " NAG A 605 " - " ASN A 446 " " NAG A 606 " - " ASN A 391 " " NAG A 607 " - " ASN A 385 " " NAG A 608 " - " ASN A 88 " " NAG A 609 " - " ASN A 148 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG B 803 " - " ASN B 637 " " NAG C 601 " - " ASN C 152 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 331 " " NAG C 605 " - " ASN C 446 " " NAG C 606 " - " ASN C 391 " " NAG C 607 " - " ASN C 385 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 148 " " NAG D 801 " - " ASN D 625 " " NAG D 802 " - " ASN D 618 " " NAG D 803 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 331 " " NAG E 605 " - " ASN E 446 " " NAG E 606 " - " ASN E 391 " " NAG E 607 " - " ASN E 385 " " NAG E 608 " - " ASN E 88 " " NAG E 609 " - " ASN E 148 " " NAG F 801 " - " ASN F 625 " " NAG F 802 " - " ASN F 618 " " NAG F 803 " - " ASN F 637 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 354 " " NAG K 1 " - " ASN C 234 " " NAG L 1 " - " ASN C 354 " " NAG N 1 " - " ASN E 234 " " NAG O 1 " - " ASN E 354 " NAG-SER " NAG G 1 " - " SER A 445 " " NAG J 1 " - " SER C 445 " " NAG M 1 " - " SER E 445 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 523.2 milliseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 24.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.936A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.694A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.086A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 660 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 333 through 352 removed outlier: 3.971A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.558A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 539 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN F 551 " --> pdb=" O GLY F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 558 Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 4.085A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.264A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (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 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE A 151 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU A 260 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU A 450 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 441 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 445 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 328 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'C' and resid 492 through 497 removed outlier: 6.107A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE C 151 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.824A pdb=" N LEU C 260 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU C 450 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 441 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 445 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 328 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.204A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE E 151 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU E 260 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU E 450 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 441 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER E 445 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA E 328 " --> pdb=" O CYS E 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 421 through 423 441 hydrogen bonds defined for protein. 1245 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: 2.40 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4603 1.34 - 1.46: 3045 1.46 - 1.57: 7190 1.57 - 1.69: 3 1.69 - 1.81: 132 Bond restraints: 14973 Sorted by residual: bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.335 1.376 -0.041 9.40e-03 1.13e+04 1.88e+01 bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.83e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.80e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.594 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.593 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 14968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19425 2.35 - 4.69: 731 4.69 - 7.04: 136 7.04 - 9.39: 24 9.39 - 11.74: 15 Bond angle restraints: 20331 Sorted by residual: angle pdb=" C MET E 153 " pdb=" N THR E 154 " pdb=" CA THR E 154 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C MET C 153 " pdb=" N THR C 154 " pdb=" CA THR C 154 " ideal model delta sigma weight residual 121.54 133.26 -11.72 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C MET A 153 " pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" CA SER F 612 " pdb=" C SER F 612 " pdb=" O SER F 612 " ideal model delta sigma weight residual 118.91 109.69 9.22 1.60e+00 3.91e-01 3.32e+01 angle pdb=" CA SER D 612 " pdb=" C SER D 612 " pdb=" O SER D 612 " ideal model delta sigma weight residual 118.91 109.73 9.18 1.60e+00 3.91e-01 3.29e+01 ... (remaining 20326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 9048 22.33 - 44.66: 582 44.66 - 66.99: 117 66.99 - 89.32: 63 89.32 - 111.65: 24 Dihedral angle restraints: 9834 sinusoidal: 4719 harmonic: 5115 Sorted by residual: 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 93.00 172.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.31 -79.31 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 9831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2344 0.114 - 0.227: 119 0.227 - 0.341: 9 0.341 - 0.455: 15 0.455 - 0.568: 3 Chirality restraints: 2490 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 2487 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 609 " -0.265 2.00e-02 2.50e+03 2.22e-01 6.13e+02 pdb=" C7 NAG E 609 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG E 609 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 609 " 0.371 2.00e-02 2.50e+03 pdb=" O7 NAG E 609 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 609 " -0.256 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG C 609 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C 609 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C 609 " 0.357 2.00e-02 2.50e+03 pdb=" O7 NAG C 609 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.242 2.00e-02 2.50e+03 2.01e-01 5.07e+02 pdb=" C7 NAG A 609 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.012 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 230 2.55 - 3.14: 11369 3.14 - 3.72: 23109 3.72 - 4.31: 30743 4.31 - 4.90: 48887 Nonbonded interactions: 114338 Sorted by model distance: nonbonded pdb=" O ASP C 367 " pdb=" N GLU C 369 " model vdw 1.959 3.120 nonbonded pdb=" O3 NAG A 609 " pdb=" O7 NAG A 609 " model vdw 2.053 3.040 nonbonded pdb=" O3 NAG C 609 " pdb=" O7 NAG C 609 " model vdw 2.060 3.040 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 2.070 3.040 nonbonded pdb=" ND2 ASN E 362 " pdb=" O THR E 371 " model vdw 2.196 3.120 ... (remaining 114333 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } 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: 3.450 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.008 0.075 15066 Z= 0.392 Angle : 1.171 13.256 20568 Z= 0.604 Chirality : 0.070 0.568 2490 Planarity : 0.009 0.222 2520 Dihedral : 17.367 111.646 6420 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.30 % Favored : 88.47 % Rotamer: Outliers : 0.97 % Allowed : 7.52 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -5.17 (0.16), residues: 1734 helix: -3.87 (0.12), residues: 405 sheet: -2.56 (0.22), residues: 474 loop : -3.75 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 158 TYR 0.015 0.002 TYR C 165 PHE 0.013 0.002 PHE A 93 TRP 0.018 0.002 TRP C 394 HIS 0.010 0.002 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00781 (14973) covalent geometry : angle 1.10783 (20331) SS BOND : bond 0.00554 ( 30) SS BOND : angle 0.82746 ( 60) hydrogen bonds : bond 0.29926 ( 441) hydrogen bonds : angle 9.86406 ( 1245) Misc. bond : bond 0.00455 ( 3) link_BETA1-4 : bond 0.01422 ( 15) link_BETA1-4 : angle 6.32654 ( 45) link_NAG-ASN : bond 0.00674 ( 42) link_NAG-ASN : angle 3.28601 ( 126) link_NAG-SER : bond 0.00572 ( 3) link_NAG-SER : angle 2.48703 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.5687 (ttt) cc_final: 0.4700 (ttm) REVERT: B 567 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7901 (mmtm) REVERT: B 601 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8586 (mtmm) REVERT: B 632 GLU cc_start: 0.9368 (tp30) cc_final: 0.9099 (tp30) REVERT: B 651 ASN cc_start: 0.9048 (t0) cc_final: 0.8827 (t0) REVERT: B 657 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8776 (mt-10) REVERT: C 69 TRP cc_start: 0.9256 (m-90) cc_final: 0.8715 (m-90) REVERT: C 424 MET cc_start: 0.5931 (ttt) cc_final: 0.4320 (ttm) REVERT: C 447 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9249 (mp) REVERT: D 601 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8465 (mtmm) REVERT: D 632 GLU cc_start: 0.9328 (tp30) cc_final: 0.8971 (tp30) REVERT: D 657 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8691 (mt-10) REVERT: E 69 TRP cc_start: 0.9174 (m-90) cc_final: 0.8697 (m-90) REVERT: E 264 SER cc_start: 0.9099 (t) cc_final: 0.8762 (m) REVERT: F 601 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8276 (mtmm) REVERT: F 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.8969 (tp30) REVERT: F 633 LYS cc_start: 0.9730 (mttt) cc_final: 0.9454 (mttp) REVERT: F 651 ASN cc_start: 0.9097 (t0) cc_final: 0.8681 (t0) REVERT: F 657 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8727 (mt-10) outliers start: 15 outliers final: 9 residues processed: 194 average time/residue: 0.1457 time to fit residues: 40.0625 Evaluate side-chains 119 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 295 ASN A 300 ASN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS B 550 GLN B 551 GLN B 564 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 276 ASN C 295 ASN C 300 ASN C 373 HIS D 550 GLN D 551 GLN D 564 HIS D 656 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 ASN E 295 ASN E 300 ASN E 373 HIS F 550 GLN F 551 GLN F 564 HIS F 575 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.041168 restraints weight = 94087.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.042265 restraints weight = 59075.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.043065 restraints weight = 44022.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043646 restraints weight = 36005.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.044039 restraints weight = 31014.832| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15066 Z= 0.185 Angle : 0.871 10.223 20568 Z= 0.418 Chirality : 0.053 0.341 2490 Planarity : 0.004 0.042 2520 Dihedral : 13.562 81.895 3132 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 2.46 % Allowed : 10.96 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -3.81 (0.18), residues: 1734 helix: -1.63 (0.22), residues: 408 sheet: -2.04 (0.23), residues: 432 loop : -3.30 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 427 TYR 0.017 0.002 TYR C 383 PHE 0.010 0.001 PHE C 93 TRP 0.017 0.002 TRP B 631 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00388 (14973) covalent geometry : angle 0.82363 (20331) SS BOND : bond 0.00142 ( 30) SS BOND : angle 0.45389 ( 60) hydrogen bonds : bond 0.05339 ( 441) hydrogen bonds : angle 6.54884 ( 1245) Misc. bond : bond 0.00093 ( 3) link_BETA1-4 : bond 0.01126 ( 15) link_BETA1-4 : angle 4.47327 ( 45) link_NAG-ASN : bond 0.00447 ( 42) link_NAG-ASN : angle 2.63756 ( 126) link_NAG-SER : bond 0.00459 ( 3) link_NAG-SER : angle 1.13897 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9073 (pp) REVERT: A 362 ASN cc_start: 0.7407 (t0) cc_final: 0.7160 (t0) REVERT: A 424 MET cc_start: 0.5844 (ttt) cc_final: 0.4867 (ttm) REVERT: B 632 GLU cc_start: 0.9351 (tp30) cc_final: 0.9007 (tp30) REVERT: B 651 ASN cc_start: 0.9131 (t0) cc_final: 0.8798 (t0) REVERT: B 657 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8751 (mt-10) REVERT: C 69 TRP cc_start: 0.9267 (m-90) cc_final: 0.8688 (m-90) REVERT: C 271 MET cc_start: 0.8559 (mmm) cc_final: 0.8261 (mmm) REVERT: C 432 MET cc_start: 0.8498 (ppp) cc_final: 0.8278 (ppp) REVERT: D 530 MET cc_start: 0.6959 (mtm) cc_final: 0.6733 (mtp) REVERT: D 574 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8858 (ptmt) REVERT: D 584 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8136 (mp0) REVERT: D 601 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8365 (mtmm) REVERT: D 632 GLU cc_start: 0.9305 (tp30) cc_final: 0.8967 (tp30) REVERT: D 657 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8684 (mt-10) REVERT: E 69 TRP cc_start: 0.9237 (m-90) cc_final: 0.8609 (m-90) REVERT: E 264 SER cc_start: 0.9105 (t) cc_final: 0.8786 (m) REVERT: E 424 MET cc_start: 0.5891 (ttt) cc_final: 0.4875 (ttm) REVERT: F 601 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8088 (mtmm) REVERT: F 632 GLU cc_start: 0.9309 (tp30) cc_final: 0.9006 (tp30) REVERT: F 633 LYS cc_start: 0.9776 (mttt) cc_final: 0.9549 (mttp) REVERT: F 651 ASN cc_start: 0.9113 (t0) cc_final: 0.8802 (t0) REVERT: F 654 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7968 (tm-30) REVERT: F 657 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8717 (mt-10) outliers start: 38 outliers final: 14 residues processed: 159 average time/residue: 0.1296 time to fit residues: 30.3705 Evaluate side-chains 128 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 99 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 362 ASN B 564 HIS B 575 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.051340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041054 restraints weight = 95157.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.042161 restraints weight = 58680.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.042968 restraints weight = 43122.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.043514 restraints weight = 35108.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.043887 restraints weight = 30557.205| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15066 Z= 0.180 Angle : 0.802 9.599 20568 Z= 0.384 Chirality : 0.051 0.305 2490 Planarity : 0.004 0.033 2520 Dihedral : 11.299 60.794 3127 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.05 % Favored : 87.77 % Rotamer: Outliers : 3.24 % Allowed : 14.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.18 (0.19), residues: 1734 helix: -0.79 (0.25), residues: 420 sheet: -1.85 (0.23), residues: 432 loop : -2.99 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 273 TYR 0.009 0.001 TYR C 383 PHE 0.012 0.001 PHE C 93 TRP 0.019 0.002 TRP B 571 HIS 0.005 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00382 (14973) covalent geometry : angle 0.75740 (20331) SS BOND : bond 0.00174 ( 30) SS BOND : angle 0.52092 ( 60) hydrogen bonds : bond 0.04691 ( 441) hydrogen bonds : angle 6.07878 ( 1245) Misc. bond : bond 0.00103 ( 3) link_BETA1-4 : bond 0.01199 ( 15) link_BETA1-4 : angle 4.25422 ( 45) link_NAG-ASN : bond 0.00454 ( 42) link_NAG-ASN : angle 2.39801 ( 126) link_NAG-SER : bond 0.00635 ( 3) link_NAG-SER : angle 1.71513 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9078 (pp) REVERT: A 424 MET cc_start: 0.5746 (ttt) cc_final: 0.4514 (ttm) REVERT: A 432 MET cc_start: 0.8439 (ppp) cc_final: 0.8210 (ppp) REVERT: B 574 LYS cc_start: 0.9321 (mmmt) cc_final: 0.8940 (ptmt) REVERT: B 632 GLU cc_start: 0.9293 (tp30) cc_final: 0.9064 (tp30) REVERT: B 651 ASN cc_start: 0.9124 (t0) cc_final: 0.8833 (t0) REVERT: B 654 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 657 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8716 (mt-10) REVERT: C 69 TRP cc_start: 0.9280 (m-90) cc_final: 0.8699 (m-90) REVERT: C 271 MET cc_start: 0.8586 (mmm) cc_final: 0.8322 (mmm) REVERT: C 447 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9162 (mp) REVERT: D 530 MET cc_start: 0.7041 (mtm) cc_final: 0.6695 (mtm) REVERT: D 574 LYS cc_start: 0.9312 (mmmt) cc_final: 0.8990 (ptmt) REVERT: D 601 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8438 (mtmm) REVERT: D 632 GLU cc_start: 0.9294 (tp30) cc_final: 0.9002 (tp30) REVERT: D 657 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8664 (mt-10) REVERT: E 69 TRP cc_start: 0.9234 (m-90) cc_final: 0.8606 (m-90) REVERT: E 424 MET cc_start: 0.5831 (ttt) cc_final: 0.4487 (ttm) REVERT: F 632 GLU cc_start: 0.9277 (tp30) cc_final: 0.9022 (tp30) REVERT: F 633 LYS cc_start: 0.9759 (mttt) cc_final: 0.9498 (mttp) REVERT: F 651 ASN cc_start: 0.9038 (t0) cc_final: 0.8684 (t0) REVERT: F 654 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8370 (tm-30) REVERT: F 657 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8756 (mt-10) outliers start: 50 outliers final: 27 residues processed: 167 average time/residue: 0.1278 time to fit residues: 31.4281 Evaluate side-chains 135 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 47 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 176 optimal weight: 50.0000 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 117 optimal weight: 50.0000 chunk 77 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 195 ASN B 564 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039936 restraints weight = 96601.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040988 restraints weight = 59601.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.041779 restraints weight = 44460.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.042305 restraints weight = 36216.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042669 restraints weight = 31398.970| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15066 Z= 0.267 Angle : 0.844 9.461 20568 Z= 0.407 Chirality : 0.051 0.278 2490 Planarity : 0.004 0.073 2520 Dihedral : 10.139 58.948 3124 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.84 % Favored : 85.99 % Rotamer: Outliers : 3.89 % Allowed : 16.28 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -3.04 (0.19), residues: 1734 helix: -0.16 (0.26), residues: 399 sheet: -1.83 (0.23), residues: 426 loop : -3.08 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 427 TYR 0.007 0.001 TYR E 316 PHE 0.016 0.002 PHE C 93 TRP 0.017 0.002 TRP B 571 HIS 0.004 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00575 (14973) covalent geometry : angle 0.80599 (20331) SS BOND : bond 0.00259 ( 30) SS BOND : angle 0.63086 ( 60) hydrogen bonds : bond 0.04491 ( 441) hydrogen bonds : angle 5.95117 ( 1245) Misc. bond : bond 0.00109 ( 3) link_BETA1-4 : bond 0.01038 ( 15) link_BETA1-4 : angle 4.02022 ( 45) link_NAG-ASN : bond 0.00442 ( 42) link_NAG-ASN : angle 2.30265 ( 126) link_NAG-SER : bond 0.00485 ( 3) link_NAG-SER : angle 1.93372 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 119 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9053 (pp) REVERT: A 362 ASN cc_start: 0.7600 (t0) cc_final: 0.7332 (t0) REVERT: A 424 MET cc_start: 0.5783 (ttt) cc_final: 0.5037 (ttm) REVERT: A 432 MET cc_start: 0.8625 (ppp) cc_final: 0.8336 (ppp) REVERT: B 574 LYS cc_start: 0.9357 (mmmt) cc_final: 0.9009 (ptpt) REVERT: B 651 ASN cc_start: 0.9241 (t0) cc_final: 0.9009 (t0) REVERT: B 654 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 657 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8748 (mt-10) REVERT: C 69 TRP cc_start: 0.9301 (m-90) cc_final: 0.8671 (m-90) REVERT: C 432 MET cc_start: 0.8743 (ppp) cc_final: 0.8423 (ppp) REVERT: C 447 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9281 (mp) REVERT: D 530 MET cc_start: 0.7547 (mtm) cc_final: 0.7201 (mtm) REVERT: D 574 LYS cc_start: 0.9344 (mmmt) cc_final: 0.9062 (ptmt) REVERT: D 632 GLU cc_start: 0.9273 (tp30) cc_final: 0.9051 (tp30) REVERT: D 633 LYS cc_start: 0.9701 (mtpp) cc_final: 0.9499 (mttp) REVERT: D 657 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8674 (mt-10) REVERT: E 69 TRP cc_start: 0.9216 (m-90) cc_final: 0.8558 (m-90) REVERT: E 432 MET cc_start: 0.8720 (ppp) cc_final: 0.8459 (ppp) REVERT: F 584 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8294 (mt-10) REVERT: F 601 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8655 (ptpp) REVERT: F 632 GLU cc_start: 0.9255 (tp30) cc_final: 0.9049 (tp30) REVERT: F 633 LYS cc_start: 0.9744 (mttt) cc_final: 0.9514 (mttp) REVERT: F 651 ASN cc_start: 0.9217 (t0) cc_final: 0.8927 (t0) REVERT: F 654 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8224 (tm-30) REVERT: F 657 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8711 (mt-10) outliers start: 60 outliers final: 45 residues processed: 168 average time/residue: 0.1313 time to fit residues: 32.5022 Evaluate side-chains 152 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 68 optimal weight: 0.3980 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.040975 restraints weight = 95858.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.042103 restraints weight = 58974.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.042937 restraints weight = 43434.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043485 restraints weight = 35139.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.043903 restraints weight = 30404.631| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15066 Z= 0.126 Angle : 0.760 9.646 20568 Z= 0.363 Chirality : 0.050 0.304 2490 Planarity : 0.004 0.079 2520 Dihedral : 9.286 59.069 3123 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.96 % Favored : 88.93 % Rotamer: Outliers : 2.72 % Allowed : 18.68 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.76 (0.20), residues: 1734 helix: -0.15 (0.27), residues: 414 sheet: -1.64 (0.25), residues: 399 loop : -2.81 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 617 TYR 0.007 0.001 TYR C 383 PHE 0.010 0.001 PHE E 360 TRP 0.022 0.001 TRP B 571 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00259 (14973) covalent geometry : angle 0.71951 (20331) SS BOND : bond 0.00155 ( 30) SS BOND : angle 0.37806 ( 60) hydrogen bonds : bond 0.04055 ( 441) hydrogen bonds : angle 5.74244 ( 1245) Misc. bond : bond 0.00100 ( 3) link_BETA1-4 : bond 0.01091 ( 15) link_BETA1-4 : angle 3.98307 ( 45) link_NAG-ASN : bond 0.00409 ( 42) link_NAG-ASN : angle 2.17815 ( 126) link_NAG-SER : bond 0.00719 ( 3) link_NAG-SER : angle 1.97126 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 362 ASN cc_start: 0.7476 (t0) cc_final: 0.7186 (t0) REVERT: A 424 MET cc_start: 0.5925 (ttt) cc_final: 0.5152 (ttm) REVERT: A 432 MET cc_start: 0.8485 (ppp) cc_final: 0.8212 (ppp) REVERT: B 626 MET cc_start: 0.8557 (ttm) cc_final: 0.8233 (ttm) REVERT: B 651 ASN cc_start: 0.9129 (t0) cc_final: 0.8898 (t0) REVERT: B 657 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8766 (mt-10) REVERT: C 69 TRP cc_start: 0.9291 (m-90) cc_final: 0.8763 (m-90) REVERT: C 113 ASP cc_start: 0.9183 (m-30) cc_final: 0.8902 (m-30) REVERT: C 432 MET cc_start: 0.8631 (ppp) cc_final: 0.8295 (ppp) REVERT: D 601 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8428 (ptpp) REVERT: D 632 GLU cc_start: 0.9282 (tp30) cc_final: 0.9052 (tp30) REVERT: D 633 LYS cc_start: 0.9704 (mtpp) cc_final: 0.9427 (mttp) REVERT: D 657 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8663 (mt-10) REVERT: E 69 TRP cc_start: 0.9172 (m-90) cc_final: 0.8663 (m-90) REVERT: E 125 LEU cc_start: 0.9674 (tp) cc_final: 0.9202 (tt) REVERT: E 153 MET cc_start: 0.7320 (tpt) cc_final: 0.7045 (tpp) REVERT: F 601 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8602 (ptpp) REVERT: F 632 GLU cc_start: 0.9293 (tp30) cc_final: 0.9080 (tp30) REVERT: F 633 LYS cc_start: 0.9752 (mttt) cc_final: 0.9521 (mttp) REVERT: F 651 ASN cc_start: 0.9091 (t0) cc_final: 0.8869 (t0) REVERT: F 654 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 655 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8880 (mmmt) REVERT: F 657 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8695 (mt-10) outliers start: 42 outliers final: 32 residues processed: 160 average time/residue: 0.1190 time to fit residues: 28.8577 Evaluate side-chains 146 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040564 restraints weight = 94074.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041728 restraints weight = 57392.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042483 restraints weight = 41928.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.043076 restraints weight = 34020.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043496 restraints weight = 29179.882| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15066 Z= 0.160 Angle : 0.753 9.523 20568 Z= 0.360 Chirality : 0.049 0.281 2490 Planarity : 0.004 0.067 2520 Dihedral : 8.958 57.268 3120 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.34 % Favored : 87.60 % Rotamer: Outliers : 3.89 % Allowed : 18.61 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.76 (0.19), residues: 1734 helix: -0.11 (0.27), residues: 417 sheet: -1.60 (0.23), residues: 432 loop : -2.89 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 557 TYR 0.007 0.001 TYR A 217 PHE 0.009 0.001 PHE C 93 TRP 0.017 0.001 TRP F 571 HIS 0.002 0.001 HIS E 351 Details of bonding type rmsd covalent geometry : bond 0.00342 (14973) covalent geometry : angle 0.71659 (20331) SS BOND : bond 0.00172 ( 30) SS BOND : angle 0.43072 ( 60) hydrogen bonds : bond 0.03880 ( 441) hydrogen bonds : angle 5.63484 ( 1245) Misc. bond : bond 0.00100 ( 3) link_BETA1-4 : bond 0.01047 ( 15) link_BETA1-4 : angle 3.78871 ( 45) link_NAG-ASN : bond 0.00354 ( 42) link_NAG-ASN : angle 2.07534 ( 126) link_NAG-SER : bond 0.00592 ( 3) link_NAG-SER : angle 1.98711 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 0.455 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: A 107 ASP cc_start: 0.8735 (m-30) cc_final: 0.8455 (t0) REVERT: A 260 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 362 ASN cc_start: 0.7531 (t0) cc_final: 0.7254 (t0) REVERT: A 424 MET cc_start: 0.6403 (ttt) cc_final: 0.5652 (ttm) REVERT: A 432 MET cc_start: 0.8549 (ppp) cc_final: 0.8248 (ppp) REVERT: B 651 ASN cc_start: 0.9157 (t0) cc_final: 0.8935 (t0) REVERT: B 657 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8744 (mt-10) REVERT: C 69 TRP cc_start: 0.9298 (m-90) cc_final: 0.8767 (m-90) REVERT: C 113 ASP cc_start: 0.9197 (m-30) cc_final: 0.8936 (m-30) REVERT: C 432 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8249 (ppp) REVERT: D 530 MET cc_start: 0.6799 (mtm) cc_final: 0.6412 (mtm) REVERT: D 601 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8586 (ptpp) REVERT: D 633 LYS cc_start: 0.9701 (mtpp) cc_final: 0.9437 (mttp) REVERT: D 657 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8670 (mt-10) REVERT: E 69 TRP cc_start: 0.9203 (m-90) cc_final: 0.8657 (m-90) REVERT: E 271 MET cc_start: 0.8208 (tpp) cc_final: 0.7965 (tpp) REVERT: E 424 MET cc_start: 0.6267 (ttt) cc_final: 0.5492 (ttm) REVERT: F 601 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8697 (ptpp) REVERT: F 633 LYS cc_start: 0.9755 (mttt) cc_final: 0.9512 (mttp) REVERT: F 651 ASN cc_start: 0.9121 (t0) cc_final: 0.8854 (t0) REVERT: F 654 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8336 (tm-30) REVERT: F 657 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8721 (mt-10) outliers start: 60 outliers final: 45 residues processed: 165 average time/residue: 0.1300 time to fit residues: 31.7970 Evaluate side-chains 158 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 ARG Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 127 optimal weight: 0.0070 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN A 423 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.040333 restraints weight = 95872.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041506 restraints weight = 59835.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.042279 restraints weight = 43879.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.042855 restraints weight = 35530.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043263 restraints weight = 30678.754| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15066 Z= 0.162 Angle : 0.754 9.506 20568 Z= 0.362 Chirality : 0.049 0.286 2490 Planarity : 0.003 0.059 2520 Dihedral : 8.761 57.270 3120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.82 % Favored : 88.00 % Rotamer: Outliers : 3.76 % Allowed : 19.84 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.70 (0.20), residues: 1734 helix: -0.09 (0.27), residues: 420 sheet: -1.60 (0.25), residues: 399 loop : -2.80 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 557 TYR 0.007 0.001 TYR A 217 PHE 0.009 0.001 PHE C 93 TRP 0.027 0.001 TRP F 571 HIS 0.002 0.001 HIS E 351 Details of bonding type rmsd covalent geometry : bond 0.00348 (14973) covalent geometry : angle 0.71945 (20331) SS BOND : bond 0.00173 ( 30) SS BOND : angle 0.42097 ( 60) hydrogen bonds : bond 0.03789 ( 441) hydrogen bonds : angle 5.53543 ( 1245) Misc. bond : bond 0.00093 ( 3) link_BETA1-4 : bond 0.01063 ( 15) link_BETA1-4 : angle 3.75464 ( 45) link_NAG-ASN : bond 0.00346 ( 42) link_NAG-ASN : angle 2.02307 ( 126) link_NAG-SER : bond 0.00553 ( 3) link_NAG-SER : angle 1.92721 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8690 (m-30) cc_final: 0.8385 (t0) REVERT: A 260 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8892 (pp) REVERT: A 424 MET cc_start: 0.6781 (ttt) cc_final: 0.5962 (ttm) REVERT: A 432 MET cc_start: 0.8600 (ppp) cc_final: 0.8289 (ppp) REVERT: B 651 ASN cc_start: 0.9167 (t0) cc_final: 0.8920 (t0) REVERT: B 657 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8751 (mt-10) REVERT: C 69 TRP cc_start: 0.9288 (m-90) cc_final: 0.8763 (m-90) REVERT: C 113 ASP cc_start: 0.9227 (m-30) cc_final: 0.8991 (m-30) REVERT: C 432 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8265 (ppp) REVERT: D 530 MET cc_start: 0.6854 (mtm) cc_final: 0.6515 (mtm) REVERT: D 601 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8479 (ptpp) REVERT: D 633 LYS cc_start: 0.9699 (mtpp) cc_final: 0.9374 (mttp) REVERT: D 657 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8653 (mt-10) REVERT: E 69 TRP cc_start: 0.9206 (m-90) cc_final: 0.8675 (m-90) REVERT: E 271 MET cc_start: 0.8213 (tpp) cc_final: 0.8001 (tpp) REVERT: E 424 MET cc_start: 0.6272 (ttt) cc_final: 0.5443 (ttm) REVERT: F 601 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8725 (ptpp) REVERT: F 633 LYS cc_start: 0.9748 (mttt) cc_final: 0.9459 (mttp) REVERT: F 651 ASN cc_start: 0.9131 (t0) cc_final: 0.8888 (t0) REVERT: F 654 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8425 (tm-30) REVERT: F 657 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8833 (mt-10) outliers start: 58 outliers final: 49 residues processed: 164 average time/residue: 0.1196 time to fit residues: 29.7789 Evaluate side-chains 163 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 114 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 117 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** 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 = 0.3203 r_free = 0.3203 target = 0.049777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039601 restraints weight = 97510.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.040741 restraints weight = 60176.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.041533 restraints weight = 43831.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042053 restraints weight = 35384.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.042443 restraints weight = 30543.258| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15066 Z= 0.235 Angle : 0.815 9.919 20568 Z= 0.394 Chirality : 0.050 0.263 2490 Planarity : 0.004 0.058 2520 Dihedral : 8.796 57.521 3120 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.55 % Favored : 86.27 % Rotamer: Outliers : 4.15 % Allowed : 20.17 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -2.66 (0.20), residues: 1734 helix: -0.08 (0.27), residues: 420 sheet: -1.58 (0.24), residues: 414 loop : -2.77 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 557 TYR 0.008 0.001 TYR A 217 PHE 0.013 0.001 PHE C 93 TRP 0.029 0.002 TRP F 571 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00509 (14973) covalent geometry : angle 0.78297 (20331) SS BOND : bond 0.00230 ( 30) SS BOND : angle 0.50490 ( 60) hydrogen bonds : bond 0.03968 ( 441) hydrogen bonds : angle 5.55982 ( 1245) Misc. bond : bond 0.00092 ( 3) link_BETA1-4 : bond 0.01004 ( 15) link_BETA1-4 : angle 3.72571 ( 45) link_NAG-ASN : bond 0.00388 ( 42) link_NAG-ASN : angle 2.04231 ( 126) link_NAG-SER : bond 0.00424 ( 3) link_NAG-SER : angle 2.00452 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 114 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 424 MET cc_start: 0.6746 (ttt) cc_final: 0.6253 (ttm) REVERT: A 432 MET cc_start: 0.8718 (ppp) cc_final: 0.8437 (ppp) REVERT: B 651 ASN cc_start: 0.8934 (t0) cc_final: 0.8624 (t0) REVERT: B 657 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 69 TRP cc_start: 0.9263 (m-90) cc_final: 0.8719 (m-90) REVERT: C 113 ASP cc_start: 0.9224 (m-30) cc_final: 0.8966 (m-30) REVERT: C 432 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8328 (ppp) REVERT: D 530 MET cc_start: 0.7218 (mtm) cc_final: 0.6930 (mtm) REVERT: D 601 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8483 (ttpp) REVERT: D 633 LYS cc_start: 0.9702 (mtpp) cc_final: 0.9371 (mttp) REVERT: D 657 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8728 (mt-10) REVERT: E 69 TRP cc_start: 0.9173 (m-90) cc_final: 0.8567 (m-90) REVERT: E 271 MET cc_start: 0.8265 (tpp) cc_final: 0.8050 (tpp) REVERT: E 424 MET cc_start: 0.6312 (ttt) cc_final: 0.5391 (ttm) REVERT: F 601 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8762 (ptpp) REVERT: F 633 LYS cc_start: 0.9758 (mttt) cc_final: 0.9487 (mttp) REVERT: F 651 ASN cc_start: 0.9136 (t0) cc_final: 0.8906 (t0) REVERT: F 654 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8507 (tm-30) REVERT: F 657 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8810 (mt-10) outliers start: 64 outliers final: 53 residues processed: 165 average time/residue: 0.1217 time to fit residues: 30.3805 Evaluate side-chains 165 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 14 optimal weight: 0.4980 chunk 166 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.040081 restraints weight = 97349.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.041229 restraints weight = 59756.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041978 restraints weight = 43661.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.042547 restraints weight = 35492.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042939 restraints weight = 30504.256| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15066 Z= 0.181 Angle : 0.793 9.767 20568 Z= 0.384 Chirality : 0.050 0.277 2490 Planarity : 0.004 0.074 2520 Dihedral : 8.680 57.352 3120 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.51 % Favored : 87.31 % Rotamer: Outliers : 3.83 % Allowed : 20.56 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -2.71 (0.20), residues: 1734 helix: -0.24 (0.27), residues: 426 sheet: -1.63 (0.25), residues: 399 loop : -2.73 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 427 TYR 0.009 0.001 TYR C 217 PHE 0.010 0.001 PHE C 93 TRP 0.032 0.001 TRP F 571 HIS 0.002 0.001 HIS E 351 Details of bonding type rmsd covalent geometry : bond 0.00390 (14973) covalent geometry : angle 0.75992 (20331) SS BOND : bond 0.00180 ( 30) SS BOND : angle 0.44581 ( 60) hydrogen bonds : bond 0.03886 ( 441) hydrogen bonds : angle 5.56707 ( 1245) Misc. bond : bond 0.00080 ( 3) link_BETA1-4 : bond 0.01024 ( 15) link_BETA1-4 : angle 3.77244 ( 45) link_NAG-ASN : bond 0.00341 ( 42) link_NAG-ASN : angle 2.02129 ( 126) link_NAG-SER : bond 0.00634 ( 3) link_NAG-SER : angle 2.31145 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 0.480 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 260 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8881 (pp) REVERT: A 424 MET cc_start: 0.6912 (ttt) cc_final: 0.6145 (ttm) REVERT: A 432 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8335 (ppp) REVERT: B 544 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 651 ASN cc_start: 0.8910 (t0) cc_final: 0.8615 (t0) REVERT: B 657 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8764 (mt-10) REVERT: C 69 TRP cc_start: 0.9285 (m-90) cc_final: 0.8776 (m-90) REVERT: C 113 ASP cc_start: 0.9190 (m-30) cc_final: 0.8921 (m-30) REVERT: C 432 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8304 (ppp) REVERT: D 530 MET cc_start: 0.7068 (mtm) cc_final: 0.6758 (mtm) REVERT: D 601 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8508 (ptpp) REVERT: D 633 LYS cc_start: 0.9696 (mtpp) cc_final: 0.9368 (mttp) REVERT: D 657 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8750 (mt-10) REVERT: E 69 TRP cc_start: 0.9186 (m-90) cc_final: 0.8660 (m-90) REVERT: F 530 MET cc_start: 0.7389 (mtm) cc_final: 0.7057 (pmm) REVERT: F 601 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8786 (ptpp) REVERT: F 633 LYS cc_start: 0.9750 (mttt) cc_final: 0.9536 (mttp) REVERT: F 651 ASN cc_start: 0.9077 (t0) cc_final: 0.8840 (t0) REVERT: F 654 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8489 (tm-30) REVERT: F 657 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8852 (mt-10) outliers start: 59 outliers final: 53 residues processed: 163 average time/residue: 0.1141 time to fit residues: 28.6851 Evaluate side-chains 171 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 114 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** 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 = 0.3234 r_free = 0.3234 target = 0.050791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.040569 restraints weight = 95838.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.041680 restraints weight = 59148.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042511 restraints weight = 43575.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.043084 restraints weight = 34942.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043507 restraints weight = 29990.097| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15066 Z= 0.141 Angle : 0.761 10.648 20568 Z= 0.366 Chirality : 0.049 0.284 2490 Planarity : 0.003 0.068 2520 Dihedral : 8.409 57.431 3120 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.05 % Favored : 87.77 % Rotamer: Outliers : 3.44 % Allowed : 21.14 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.65 (0.20), residues: 1734 helix: -0.22 (0.27), residues: 429 sheet: -1.43 (0.26), residues: 366 loop : -2.75 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 557 TYR 0.011 0.001 TYR E 217 PHE 0.008 0.001 PHE C 93 TRP 0.035 0.001 TRP F 571 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00303 (14973) covalent geometry : angle 0.72806 (20331) SS BOND : bond 0.00142 ( 30) SS BOND : angle 0.40326 ( 60) hydrogen bonds : bond 0.03600 ( 441) hydrogen bonds : angle 5.48386 ( 1245) Misc. bond : bond 0.00078 ( 3) link_BETA1-4 : bond 0.01067 ( 15) link_BETA1-4 : angle 3.71057 ( 45) link_NAG-ASN : bond 0.00321 ( 42) link_NAG-ASN : angle 1.95038 ( 126) link_NAG-SER : bond 0.00739 ( 3) link_NAG-SER : angle 2.14421 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8860 (pp) REVERT: A 424 MET cc_start: 0.6886 (ttt) cc_final: 0.6112 (ttm) REVERT: A 432 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8253 (ppp) REVERT: B 651 ASN cc_start: 0.8810 (t0) cc_final: 0.8475 (t0) REVERT: B 657 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8743 (mt-10) REVERT: C 69 TRP cc_start: 0.9272 (m-90) cc_final: 0.8850 (m-90) REVERT: C 113 ASP cc_start: 0.9113 (m-30) cc_final: 0.8848 (m-30) REVERT: C 125 LEU cc_start: 0.9604 (tp) cc_final: 0.9206 (tt) REVERT: C 432 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8229 (ppp) REVERT: D 530 MET cc_start: 0.6822 (mtm) cc_final: 0.6533 (mtm) REVERT: D 554 ASN cc_start: 0.8678 (m110) cc_final: 0.8432 (p0) REVERT: D 601 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8513 (ptpp) REVERT: D 633 LYS cc_start: 0.9685 (mtpp) cc_final: 0.9348 (mttp) REVERT: D 657 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8735 (mt-10) REVERT: E 69 TRP cc_start: 0.9194 (m-90) cc_final: 0.8725 (m-90) REVERT: E 125 LEU cc_start: 0.9625 (tp) cc_final: 0.9138 (tt) REVERT: E 424 MET cc_start: 0.6675 (ttt) cc_final: 0.5805 (ttm) REVERT: F 530 MET cc_start: 0.7168 (mtm) cc_final: 0.6946 (pmm) REVERT: F 601 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8729 (ptpp) REVERT: F 633 LYS cc_start: 0.9736 (mttt) cc_final: 0.9473 (mttp) REVERT: F 651 ASN cc_start: 0.9052 (t0) cc_final: 0.8809 (t0) REVERT: F 654 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8483 (tm-30) REVERT: F 657 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8816 (mt-10) outliers start: 53 outliers final: 47 residues processed: 165 average time/residue: 0.1228 time to fit residues: 30.8569 Evaluate side-chains 166 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 76 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 43 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.051383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.041162 restraints weight = 95126.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.042339 restraints weight = 58578.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.043157 restraints weight = 42634.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043719 restraints weight = 34298.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044123 restraints weight = 29520.415| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15066 Z= 0.122 Angle : 0.754 10.380 20568 Z= 0.361 Chirality : 0.049 0.286 2490 Planarity : 0.004 0.070 2520 Dihedral : 8.275 57.689 3120 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.13 % Favored : 88.75 % Rotamer: Outliers : 3.24 % Allowed : 21.40 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.55 (0.20), residues: 1734 helix: -0.25 (0.27), residues: 429 sheet: -0.99 (0.28), residues: 330 loop : -2.76 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 557 TYR 0.010 0.001 TYR A 217 PHE 0.009 0.001 PHE A 360 TRP 0.028 0.001 TRP F 571 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00256 (14973) covalent geometry : angle 0.72143 (20331) SS BOND : bond 0.00136 ( 30) SS BOND : angle 0.40486 ( 60) hydrogen bonds : bond 0.03567 ( 441) hydrogen bonds : angle 5.45342 ( 1245) Misc. bond : bond 0.00075 ( 3) link_BETA1-4 : bond 0.01120 ( 15) link_BETA1-4 : angle 3.67545 ( 45) link_NAG-ASN : bond 0.00332 ( 42) link_NAG-ASN : angle 1.90991 ( 126) link_NAG-SER : bond 0.00715 ( 3) link_NAG-SER : angle 2.11395 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.50 seconds wall clock time: 37 minutes 44.88 seconds (2264.88 seconds total)