Starting phenix.real_space_refine on Sun Aug 24 06:58:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szi_40917/08_2025/8szi_40917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szi_40917/08_2025/8szi_40917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8szi_40917/08_2025/8szi_40917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szi_40917/08_2025/8szi_40917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szi_40917/08_2025/8szi_40917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szi_40917/08_2025/8szi_40917.map" } resolution = 3.5 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= 0.020 sd= 0.060 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 11526 2.51 5 N 2932 2.21 5 O 3294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17868 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1765 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2509 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 6538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 826, 6524 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 32, 'TRANS': 793} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 826, 6524 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 32, 'TRANS': 793} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 6676 Chain: "B" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6327 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 31, 'TRANS': 770} Chain breaks: 3 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" 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: "G" 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: "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: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1005 "'] Classifications: {'peptide': 2, 'undetermined': 5} Modifications used: {'COO': 2} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 132 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1407 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 818 " occ=0.70 ... (26 atoms not shown) pdb=" CH2BTRP A 818 " occ=0.30 Time building chain proxies: 5.42, per 1000 atoms: 0.30 Number of scatterers: 17868 At special positions: 0 Unit cell: (99.7855, 118.007, 249.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3294 8.00 N 2932 7.00 C 11526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1002 " - " ASN A 468 " " NAG B1403 " - " ASN B 468 " " NAG B1404 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 935.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 43.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 207 through 213 removed outlier: 4.171A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.941A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.945A pdb=" N PHE C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.671A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 24 removed outlier: 3.686A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.624A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.680A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.503A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.788A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.587A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.522A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.128A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.509A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.544A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.678A pdb=" N ILE A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.633A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.646A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 673 through 678 removed outlier: 3.940A pdb=" N ARG A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 708 removed outlier: 4.040A pdb=" N ALA A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 746 removed outlier: 3.665A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.558A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 821 Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.624A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 removed outlier: 3.601A pdb=" N ARG A 866 " --> pdb=" O LYS A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 878 Processing helix chain 'B' and resid 66 through 84 removed outlier: 3.729A pdb=" N TRP B 70 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.603A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.838A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.078A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.629A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.571A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.913A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.768A pdb=" N GLY B 532 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.681A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.921A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 673 through 698 removed outlier: 4.749A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix Processing helix chain 'B' and resid 702 through 707 removed outlier: 4.399A pdb=" N PHE B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.607A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 732 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.841A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 828 removed outlier: 3.721A pdb=" N ASN B 802 " --> pdb=" O PRO B 798 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 803 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 830 through 833 Processing helix chain 'B' and resid 834 through 861 removed outlier: 3.745A pdb=" N VAL B 838 " --> pdb=" O SER B 834 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.698A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 51 removed outlier: 7.143A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.893A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.884A pdb=" N ALA D 104 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.920A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.777A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.960A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 252 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.845A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.737A pdb=" N TYR A 95 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.090A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.891A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.214A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.728A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 37 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.068A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N PHE B 320 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA B 295 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AC3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AC4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC5, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.736A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 762 " --> pdb=" O ASN B 753 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 751 " --> pdb=" O THR B 764 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2197 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: 2.97 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2887 1.32 - 1.44: 5110 1.44 - 1.57: 10126 1.57 - 1.70: 22 1.70 - 1.83: 136 Bond restraints: 18281 Sorted by residual: bond pdb=" C31 PCW B1402 " pdb=" O2 PCW B1402 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C31 PCW A1001 " pdb=" O2 PCW A1001 " ideal model delta sigma weight residual 1.333 1.485 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C ASN B 802 " pdb=" O ASN B 802 " ideal model delta sigma weight residual 1.233 1.315 -0.082 1.29e-02 6.01e+03 4.09e+01 bond pdb=" C31 PCW B1402 " pdb=" C32 PCW B1402 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C31 PCW A1001 " pdb=" C32 PCW A1001 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 18276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 24722 5.01 - 10.02: 61 10.02 - 15.03: 5 15.03 - 20.05: 2 20.05 - 25.06: 2 Bond angle restraints: 24792 Sorted by residual: angle pdb=" C18 PCW B1402 " pdb=" C19 PCW B1402 " pdb=" C20 PCW B1402 " ideal model delta sigma weight residual 127.82 152.88 -25.06 3.00e+00 1.11e-01 6.98e+01 angle pdb=" C18 PCW A1001 " pdb=" C19 PCW A1001 " pdb=" C20 PCW A1001 " ideal model delta sigma weight residual 127.82 152.77 -24.95 3.00e+00 1.11e-01 6.92e+01 angle pdb=" N ASN A 118 " pdb=" CA ASN A 118 " pdb=" C ASN A 118 " ideal model delta sigma weight residual 112.38 104.38 8.00 1.22e+00 6.72e-01 4.30e+01 angle pdb=" C GLU A 232 " pdb=" N ARG A 233 " pdb=" CA ARG A 233 " ideal model delta sigma weight residual 122.65 113.56 9.09 1.60e+00 3.91e-01 3.23e+01 angle pdb=" N PHE A 714 " pdb=" CA PHE A 714 " pdb=" C PHE A 714 " ideal model delta sigma weight residual 113.38 106.41 6.97 1.23e+00 6.61e-01 3.21e+01 ... (remaining 24787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 10219 20.83 - 41.67: 645 41.67 - 62.50: 85 62.50 - 83.34: 19 83.34 - 104.17: 7 Dihedral angle restraints: 10975 sinusoidal: 4430 harmonic: 6545 Sorted by residual: dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 177.76 -84.76 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -167.54 81.54 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -39.73 -46.27 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 10972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.037: 2803 1.037 - 2.074: 0 2.074 - 3.111: 0 3.111 - 4.148: 0 4.148 - 5.185: 1 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C2 PCW A1001 " pdb=" C1 PCW A1001 " pdb=" C3 PCW A1001 " pdb=" O2 PCW A1001 " both_signs ideal model delta sigma weight residual False -2.32 2.86 -5.19 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C2 PCW B1402 " pdb=" C1 PCW B1402 " pdb=" C3 PCW B1402 " pdb=" O2 PCW B1402 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2801 not shown) Planarity restraints: 3127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.338 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG H 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.257 2.00e-02 2.50e+03 2.16e-01 5.81e+02 pdb=" C7 NAG H 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.362 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 817 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C VAL A 817 " 0.092 2.00e-02 2.50e+03 pdb=" O VAL A 817 " -0.034 2.00e-02 2.50e+03 pdb=" N ATRP A 818 " -0.032 2.00e-02 2.50e+03 ... (remaining 3124 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 57 2.56 - 3.14: 13370 3.14 - 3.73: 25376 3.73 - 4.31: 36003 4.31 - 4.90: 61447 Nonbonded interactions: 136253 Sorted by model distance: nonbonded pdb=" O LEU A 88 " pdb="CA CA A1003 " model vdw 1.971 2.510 nonbonded pdb=" O LEU B 88 " pdb="CA CA B1405 " model vdw 2.085 2.510 nonbonded pdb=" OE2 GLU C 318 " pdb=" OH TYR C 320 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.203 3.120 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.210 3.040 ... (remaining 136248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 362 or resid 392 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 586 or \ (resid 587 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 8 through 601 or (resid 602 and (name N or name CA or name C or name O or name C \ B )) or resid 603 or (resid 604 and (name N or name CA or name C or name O or na \ me CB )) or resid 605 through 704 or (resid 705 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 708 or (resid 709 and (name N or n \ ame CA or name C or name O or name CB )) or resid 722 through 798 or (resid 799 \ and (name N or name CA or name C or name O or name CB )) or resid 800 through 81 \ 7 or resid 819 through 861 or (resid 862 through 863 and (name N or name CA or n \ ame C or name O or name CB )) or resid 864 through 865 or (resid 866 through 867 \ and (name N or name CA or name C or name O or name CB )) or resid 868 through 8 \ 70 or (resid 871 through 873 and (name N or name CA or name C or name O or name \ CB )) or resid 874 through 876 or resid 1002 through 1006)) selection = (chain 'B' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 47 or (resid 48 and (name N or name CA or name C or name \ O or name CB )) or resid 49 through 118 or (resid 119 through 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 36 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 392 through \ 498 or (resid 499 through 500 and (name N or name CA or name C or name O or name \ CB )) or resid 501 through 591 or (resid 592 and (name N or name CA or name C o \ r name O or name CB )) or resid 593 through 817 or resid 819 through 876 or resi \ d 1404 through 1408)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.30 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: 7.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.630 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 0.155 18308 Z= 0.500 Angle : 0.970 25.057 24855 Z= 0.655 Chirality : 0.117 5.185 2804 Planarity : 0.008 0.293 3121 Dihedral : 13.695 104.170 6683 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.05 % Allowed : 1.61 % Favored : 98.34 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 0.27 (0.18), residues: 2227 helix: 1.43 (0.18), residues: 871 sheet: -0.48 (0.26), residues: 383 loop : -0.63 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 551 TYR 0.038 0.001 TYR A 425 PHE 0.025 0.001 PHE A 814 TRP 0.047 0.001 TRP A 719 HIS 0.007 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00750 (18281) covalent geometry : angle 0.96560 (24792) SS BOND : bond 0.00824 ( 18) SS BOND : angle 1.76924 ( 36) hydrogen bonds : bond 0.21817 ( 760) hydrogen bonds : angle 6.30726 ( 2197) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 1.35610 ( 9) link_NAG-ASN : bond 0.00367 ( 6) link_NAG-ASN : angle 2.57753 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: C 230 TYR cc_start: 0.7454 (p90) cc_final: 0.7165 (p90) REVERT: A 58 VAL cc_start: 0.8667 (p) cc_final: 0.8425 (m) REVERT: A 189 ASN cc_start: 0.7770 (p0) cc_final: 0.7566 (p0) REVERT: A 663 SER cc_start: 0.8756 (t) cc_final: 0.8188 (p) REVERT: A 704 LEU cc_start: 0.8634 (tp) cc_final: 0.8294 (mt) REVERT: B 54 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7328 (ttm110) REVERT: B 58 VAL cc_start: 0.8156 (p) cc_final: 0.7941 (m) REVERT: B 251 GLU cc_start: 0.7293 (pt0) cc_final: 0.7063 (pt0) REVERT: B 341 LYS cc_start: 0.7588 (mtmt) cc_final: 0.7382 (mmtt) REVERT: B 357 ASN cc_start: 0.8375 (t0) cc_final: 0.8097 (t0) REVERT: B 643 VAL cc_start: 0.7562 (m) cc_final: 0.7340 (t) REVERT: B 706 PHE cc_start: 0.6185 (t80) cc_final: 0.5716 (t80) REVERT: B 771 MET cc_start: 0.5157 (mmm) cc_final: 0.4945 (mtt) outliers start: 1 outliers final: 1 residues processed: 334 average time/residue: 0.1542 time to fit residues: 75.9673 Evaluate side-chains 215 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 75 GLN D 175 GLN A 193 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 117 GLN B 463 HIS B 735 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074181 restraints weight = 73399.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076884 restraints weight = 118622.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077389 restraints weight = 46169.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077791 restraints weight = 38827.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078024 restraints weight = 34660.966| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18308 Z= 0.158 Angle : 0.570 8.739 24855 Z= 0.305 Chirality : 0.044 0.193 2804 Planarity : 0.004 0.048 3121 Dihedral : 8.244 82.414 2751 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.07 % Allowed : 6.85 % Favored : 92.08 % 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 aren not related in a simple way. whole: 0.41 (0.18), residues: 2227 helix: 1.81 (0.18), residues: 879 sheet: -0.56 (0.26), residues: 396 loop : -0.79 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 197 TYR 0.015 0.001 TYR B 421 PHE 0.028 0.002 PHE A 789 TRP 0.031 0.002 TRP A 719 HIS 0.015 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00355 (18281) covalent geometry : angle 0.56381 (24792) SS BOND : bond 0.00202 ( 18) SS BOND : angle 1.64785 ( 36) hydrogen bonds : bond 0.06630 ( 760) hydrogen bonds : angle 4.46963 ( 2197) link_BETA1-4 : bond 0.00160 ( 3) link_BETA1-4 : angle 2.10770 ( 9) link_NAG-ASN : bond 0.00196 ( 6) link_NAG-ASN : angle 1.80754 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7735 (mtm180) REVERT: D 14 LEU cc_start: 0.7308 (mm) cc_final: 0.6902 (mp) REVERT: A 657 SER cc_start: 0.8683 (t) cc_final: 0.8421 (m) REVERT: A 663 SER cc_start: 0.8711 (t) cc_final: 0.8215 (p) REVERT: A 704 LEU cc_start: 0.8392 (tp) cc_final: 0.8079 (mt) REVERT: B 58 VAL cc_start: 0.8347 (p) cc_final: 0.8003 (m) REVERT: B 636 LYS cc_start: 0.6594 (mmtt) cc_final: 0.6353 (mmtt) REVERT: B 643 VAL cc_start: 0.7686 (m) cc_final: 0.7345 (t) REVERT: B 706 PHE cc_start: 0.6113 (t80) cc_final: 0.5744 (t80) REVERT: B 814 PHE cc_start: 0.8380 (t80) cc_final: 0.8171 (t80) outliers start: 20 outliers final: 11 residues processed: 240 average time/residue: 0.1606 time to fit residues: 56.3509 Evaluate side-chains 205 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 137 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 160 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 175 GLN A 117 GLN A 193 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 357 ASN B 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073959 restraints weight = 59953.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074257 restraints weight = 79578.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074640 restraints weight = 77323.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076163 restraints weight = 48076.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076383 restraints weight = 34442.858| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18308 Z= 0.126 Angle : 0.510 7.223 24855 Z= 0.272 Chirality : 0.042 0.183 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.611 77.023 2751 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.28 % Allowed : 8.51 % Favored : 90.21 % 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 aren not related in a simple way. whole: 0.51 (0.18), residues: 2227 helix: 1.94 (0.17), residues: 881 sheet: -0.53 (0.26), residues: 396 loop : -0.79 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 340 TYR 0.014 0.001 TYR B 421 PHE 0.016 0.001 PHE C 274 TRP 0.021 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00278 (18281) covalent geometry : angle 0.50496 (24792) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.44660 ( 36) hydrogen bonds : bond 0.05541 ( 760) hydrogen bonds : angle 4.15957 ( 2197) link_BETA1-4 : bond 0.00245 ( 3) link_BETA1-4 : angle 1.37108 ( 9) link_NAG-ASN : bond 0.00180 ( 6) link_NAG-ASN : angle 1.76753 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.709 Fit side-chains REVERT: C 24 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7810 (mtm180) REVERT: D 14 LEU cc_start: 0.7396 (mm) cc_final: 0.7185 (mm) REVERT: A 657 SER cc_start: 0.8694 (t) cc_final: 0.8435 (m) REVERT: A 663 SER cc_start: 0.8708 (t) cc_final: 0.8217 (p) REVERT: A 704 LEU cc_start: 0.8472 (tp) cc_final: 0.8076 (mt) REVERT: B 58 VAL cc_start: 0.8344 (p) cc_final: 0.8024 (m) REVERT: B 643 VAL cc_start: 0.7585 (m) cc_final: 0.7276 (t) REVERT: B 688 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: B 706 PHE cc_start: 0.6235 (t80) cc_final: 0.5878 (t80) outliers start: 24 outliers final: 14 residues processed: 207 average time/residue: 0.1541 time to fit residues: 47.6608 Evaluate side-chains 200 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 187 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 175 GLN A 117 GLN A 309 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 357 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073977 restraints weight = 66907.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075881 restraints weight = 106030.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076180 restraints weight = 65725.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077878 restraints weight = 44703.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078642 restraints weight = 30851.683| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18308 Z= 0.116 Angle : 0.492 8.110 24855 Z= 0.262 Chirality : 0.041 0.173 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.084 69.477 2751 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.28 % Allowed : 9.84 % Favored : 88.87 % 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 aren not related in a simple way. whole: 0.61 (0.18), residues: 2227 helix: 2.08 (0.17), residues: 882 sheet: -0.48 (0.26), residues: 388 loop : -0.79 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.016 0.001 TYR A 744 PHE 0.027 0.001 PHE A 789 TRP 0.024 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00259 (18281) covalent geometry : angle 0.48684 (24792) SS BOND : bond 0.00154 ( 18) SS BOND : angle 1.43210 ( 36) hydrogen bonds : bond 0.04857 ( 760) hydrogen bonds : angle 3.93853 ( 2197) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.39305 ( 9) link_NAG-ASN : bond 0.00154 ( 6) link_NAG-ASN : angle 1.62343 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7793 (mtm180) REVERT: D 181 THR cc_start: 0.8082 (p) cc_final: 0.7874 (t) REVERT: D 297 TRP cc_start: 0.8288 (m100) cc_final: 0.8074 (m100) REVERT: A 570 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.6163 (t0) REVERT: A 657 SER cc_start: 0.8704 (t) cc_final: 0.8447 (m) REVERT: A 663 SER cc_start: 0.8657 (t) cc_final: 0.8187 (p) REVERT: B 58 VAL cc_start: 0.8377 (p) cc_final: 0.8077 (m) REVERT: B 688 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: B 706 PHE cc_start: 0.6237 (t80) cc_final: 0.5856 (t80) outliers start: 24 outliers final: 14 residues processed: 210 average time/residue: 0.1528 time to fit residues: 47.4127 Evaluate side-chains 202 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 8 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 180 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072618 restraints weight = 60890.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072726 restraints weight = 57835.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073440 restraints weight = 46407.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074520 restraints weight = 36338.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074727 restraints weight = 34362.278| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18308 Z= 0.109 Angle : 0.489 7.714 24855 Z= 0.259 Chirality : 0.041 0.265 2804 Planarity : 0.004 0.047 3121 Dihedral : 6.803 66.575 2751 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.50 % Allowed : 10.01 % Favored : 88.50 % 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 aren not related in a simple way. whole: 0.67 (0.18), residues: 2227 helix: 2.16 (0.17), residues: 881 sheet: -0.44 (0.26), residues: 389 loop : -0.78 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 54 TYR 0.013 0.001 TYR B 421 PHE 0.022 0.001 PHE B 814 TRP 0.019 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00239 (18281) covalent geometry : angle 0.48369 (24792) SS BOND : bond 0.00133 ( 18) SS BOND : angle 1.40632 ( 36) hydrogen bonds : bond 0.04603 ( 760) hydrogen bonds : angle 3.85652 ( 2197) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 1.34914 ( 9) link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.57629 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7889 (mtm180) REVERT: D 181 THR cc_start: 0.8159 (p) cc_final: 0.7924 (t) REVERT: D 297 TRP cc_start: 0.8306 (m100) cc_final: 0.8031 (m100) REVERT: A 61 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 570 ASP cc_start: 0.6605 (OUTLIER) cc_final: 0.6389 (t0) REVERT: A 657 SER cc_start: 0.8702 (t) cc_final: 0.8470 (m) REVERT: A 663 SER cc_start: 0.8705 (t) cc_final: 0.8170 (p) REVERT: B 58 VAL cc_start: 0.8354 (p) cc_final: 0.8076 (m) REVERT: B 270 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 688 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7129 (m-80) outliers start: 28 outliers final: 18 residues processed: 207 average time/residue: 0.1409 time to fit residues: 43.8017 Evaluate side-chains 201 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 101 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 120 optimal weight: 0.0270 chunk 71 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072933 restraints weight = 51020.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072543 restraints weight = 58769.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073255 restraints weight = 52880.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073313 restraints weight = 40024.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073471 restraints weight = 42166.723| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18308 Z= 0.115 Angle : 0.489 7.558 24855 Z= 0.259 Chirality : 0.041 0.216 2804 Planarity : 0.003 0.047 3121 Dihedral : 6.669 64.506 2751 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.55 % Allowed : 10.75 % Favored : 87.69 % 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 aren not related in a simple way. whole: 0.66 (0.18), residues: 2227 helix: 2.15 (0.17), residues: 881 sheet: -0.43 (0.26), residues: 387 loop : -0.81 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 340 TYR 0.013 0.001 TYR B 421 PHE 0.028 0.001 PHE A 789 TRP 0.014 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00260 (18281) covalent geometry : angle 0.48382 (24792) SS BOND : bond 0.00144 ( 18) SS BOND : angle 1.39997 ( 36) hydrogen bonds : bond 0.04646 ( 760) hydrogen bonds : angle 3.83841 ( 2197) link_BETA1-4 : bond 0.00211 ( 3) link_BETA1-4 : angle 1.37221 ( 9) link_NAG-ASN : bond 0.00145 ( 6) link_NAG-ASN : angle 1.59284 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7828 (mtm180) REVERT: C 29 LYS cc_start: 0.8375 (tptt) cc_final: 0.7821 (ttpp) REVERT: D 297 TRP cc_start: 0.8299 (m100) cc_final: 0.8037 (m100) REVERT: A 570 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6362 (t0) REVERT: A 657 SER cc_start: 0.8674 (t) cc_final: 0.8426 (m) REVERT: A 663 SER cc_start: 0.8685 (t) cc_final: 0.8183 (p) REVERT: B 58 VAL cc_start: 0.8345 (p) cc_final: 0.8041 (m) REVERT: B 270 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8227 (t80) REVERT: B 625 PHE cc_start: 0.6835 (t80) cc_final: 0.6591 (t80) REVERT: B 688 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7143 (m-80) outliers start: 29 outliers final: 20 residues processed: 204 average time/residue: 0.1454 time to fit residues: 44.4197 Evaluate side-chains 205 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 110 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074295 restraints weight = 76740.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076272 restraints weight = 121530.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077304 restraints weight = 48997.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078251 restraints weight = 36489.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078372 restraints weight = 28224.959| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18308 Z= 0.130 Angle : 0.509 8.088 24855 Z= 0.269 Chirality : 0.042 0.207 2804 Planarity : 0.004 0.062 3121 Dihedral : 6.605 62.203 2751 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.55 % Allowed : 11.45 % Favored : 87.00 % 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 aren not related in a simple way. whole: 0.60 (0.18), residues: 2227 helix: 2.12 (0.17), residues: 882 sheet: -0.48 (0.26), residues: 382 loop : -0.86 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 340 TYR 0.014 0.001 TYR B 421 PHE 0.026 0.001 PHE A 733 TRP 0.014 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00303 (18281) covalent geometry : angle 0.50423 (24792) SS BOND : bond 0.00165 ( 18) SS BOND : angle 1.43896 ( 36) hydrogen bonds : bond 0.04853 ( 760) hydrogen bonds : angle 3.85228 ( 2197) link_BETA1-4 : bond 0.00185 ( 3) link_BETA1-4 : angle 1.43379 ( 9) link_NAG-ASN : bond 0.00143 ( 6) link_NAG-ASN : angle 1.64773 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7823 (mtm180) REVERT: C 29 LYS cc_start: 0.8286 (tptt) cc_final: 0.7834 (ttpp) REVERT: A 516 LYS cc_start: 0.7960 (pptt) cc_final: 0.7750 (ptmm) REVERT: A 570 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.6266 (t0) REVERT: A 657 SER cc_start: 0.8667 (t) cc_final: 0.8417 (m) REVERT: A 663 SER cc_start: 0.8670 (t) cc_final: 0.8201 (p) REVERT: B 58 VAL cc_start: 0.8380 (p) cc_final: 0.8084 (m) REVERT: B 688 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: B 818 TRP cc_start: 0.8417 (m100) cc_final: 0.8119 (m100) outliers start: 29 outliers final: 24 residues processed: 208 average time/residue: 0.1553 time to fit residues: 48.2528 Evaluate side-chains 208 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 123 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 162 optimal weight: 0.0470 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** 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 = 0.3525 r_free = 0.3525 target = 0.089649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073628 restraints weight = 73690.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076357 restraints weight = 111969.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076720 restraints weight = 47484.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077870 restraints weight = 38514.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077911 restraints weight = 31944.434| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18308 Z= 0.107 Angle : 0.494 8.768 24855 Z= 0.261 Chirality : 0.041 0.190 2804 Planarity : 0.003 0.047 3121 Dihedral : 6.498 61.552 2751 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.39 % Allowed : 11.93 % Favored : 86.68 % 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 aren not related in a simple way. whole: 0.67 (0.18), residues: 2227 helix: 2.19 (0.17), residues: 882 sheet: -0.45 (0.26), residues: 382 loop : -0.83 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 340 TYR 0.013 0.001 TYR B 421 PHE 0.034 0.001 PHE A 733 TRP 0.013 0.001 TRP A 299 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00235 (18281) covalent geometry : angle 0.48927 (24792) SS BOND : bond 0.00144 ( 18) SS BOND : angle 1.36478 ( 36) hydrogen bonds : bond 0.04501 ( 760) hydrogen bonds : angle 3.79316 ( 2197) link_BETA1-4 : bond 0.00257 ( 3) link_BETA1-4 : angle 1.35121 ( 9) link_NAG-ASN : bond 0.00153 ( 6) link_NAG-ASN : angle 1.59082 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7834 (mtm180) REVERT: C 29 LYS cc_start: 0.8199 (tptt) cc_final: 0.7785 (ttpp) REVERT: C 290 TYR cc_start: 0.6442 (p90) cc_final: 0.6237 (p90) REVERT: A 570 ASP cc_start: 0.6469 (OUTLIER) cc_final: 0.6259 (t0) REVERT: A 657 SER cc_start: 0.8668 (t) cc_final: 0.8402 (m) REVERT: A 663 SER cc_start: 0.8659 (t) cc_final: 0.8211 (p) REVERT: B 58 VAL cc_start: 0.8366 (p) cc_final: 0.8088 (m) REVERT: B 688 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: B 818 TRP cc_start: 0.8406 (m100) cc_final: 0.8121 (m100) REVERT: B 819 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8181 (tp) outliers start: 26 outliers final: 22 residues processed: 204 average time/residue: 0.1505 time to fit residues: 45.7199 Evaluate side-chains 207 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 170 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070695 restraints weight = 54384.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070327 restraints weight = 59611.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070889 restraints weight = 52137.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071022 restraints weight = 41658.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071323 restraints weight = 41935.556| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18308 Z= 0.260 Angle : 0.633 9.449 24855 Z= 0.335 Chirality : 0.047 0.233 2804 Planarity : 0.004 0.072 3121 Dihedral : 6.990 60.764 2751 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.39 % Allowed : 12.15 % Favored : 86.46 % 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 aren not related in a simple way. whole: 0.17 (0.18), residues: 2227 helix: 1.63 (0.17), residues: 894 sheet: -0.61 (0.26), residues: 390 loop : -1.03 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 340 TYR 0.022 0.002 TYR B 421 PHE 0.033 0.002 PHE A 789 TRP 0.020 0.002 TRP A1005 HIS 0.012 0.002 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00641 (18281) covalent geometry : angle 0.62642 (24792) SS BOND : bond 0.00331 ( 18) SS BOND : angle 1.79214 ( 36) hydrogen bonds : bond 0.06592 ( 760) hydrogen bonds : angle 4.19394 ( 2197) link_BETA1-4 : bond 0.00359 ( 3) link_BETA1-4 : angle 1.85453 ( 9) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 2.13770 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.568 Fit side-chains REVERT: C 24 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7910 (mtm180) REVERT: C 29 LYS cc_start: 0.8403 (tptt) cc_final: 0.7906 (ttpp) REVERT: C 230 TYR cc_start: 0.7603 (p90) cc_final: 0.7221 (p90) REVERT: A 570 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6621 (t0) REVERT: A 657 SER cc_start: 0.8590 (t) cc_final: 0.8369 (m) REVERT: A 663 SER cc_start: 0.8715 (t) cc_final: 0.8228 (p) REVERT: B 197 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: B 270 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 688 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: B 818 TRP cc_start: 0.8451 (m100) cc_final: 0.8157 (m100) outliers start: 26 outliers final: 18 residues processed: 207 average time/residue: 0.1338 time to fit residues: 40.7703 Evaluate side-chains 208 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 91 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 143 optimal weight: 0.0980 chunk 192 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 214 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072999 restraints weight = 53659.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072427 restraints weight = 66072.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072946 restraints weight = 64593.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.073784 restraints weight = 44804.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073960 restraints weight = 39719.057| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18308 Z= 0.108 Angle : 0.509 8.564 24855 Z= 0.269 Chirality : 0.041 0.184 2804 Planarity : 0.004 0.046 3121 Dihedral : 6.558 59.743 2751 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.96 % Allowed : 12.73 % Favored : 86.30 % 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 aren not related in a simple way. whole: 0.54 (0.18), residues: 2227 helix: 2.09 (0.17), residues: 881 sheet: -0.53 (0.26), residues: 382 loop : -0.90 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 340 TYR 0.014 0.001 TYR B 421 PHE 0.037 0.001 PHE A 789 TRP 0.015 0.001 TRP A 299 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00232 (18281) covalent geometry : angle 0.50386 (24792) SS BOND : bond 0.00159 ( 18) SS BOND : angle 1.37371 ( 36) hydrogen bonds : bond 0.04510 ( 760) hydrogen bonds : angle 3.84626 ( 2197) link_BETA1-4 : bond 0.00240 ( 3) link_BETA1-4 : angle 1.40588 ( 9) link_NAG-ASN : bond 0.00185 ( 6) link_NAG-ASN : angle 1.79907 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8343 (tptt) cc_final: 0.7944 (ttpp) REVERT: C 243 MET cc_start: 0.7243 (tpp) cc_final: 0.7008 (tpp) REVERT: D 297 TRP cc_start: 0.8382 (m100) cc_final: 0.8073 (m100) REVERT: A 570 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6402 (t0) REVERT: A 657 SER cc_start: 0.8661 (t) cc_final: 0.8420 (m) REVERT: A 663 SER cc_start: 0.8705 (t) cc_final: 0.8167 (p) REVERT: B 270 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8287 (t80) REVERT: B 688 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7180 (m-80) outliers start: 18 outliers final: 12 residues processed: 194 average time/residue: 0.1396 time to fit residues: 40.2076 Evaluate side-chains 198 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 1 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 177 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.089205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073249 restraints weight = 55869.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072866 restraints weight = 66147.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073533 restraints weight = 55249.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.074154 restraints weight = 42604.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.074425 restraints weight = 43019.966| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18308 Z= 0.110 Angle : 0.508 8.457 24855 Z= 0.267 Chirality : 0.042 0.189 2804 Planarity : 0.004 0.078 3121 Dihedral : 6.416 58.148 2751 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 12.73 % Favored : 86.30 % 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 aren not related in a simple way. whole: 0.62 (0.18), residues: 2227 helix: 2.19 (0.17), residues: 875 sheet: -0.50 (0.26), residues: 382 loop : -0.87 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 340 TYR 0.013 0.001 TYR B 421 PHE 0.041 0.001 PHE A 789 TRP 0.014 0.001 TRP A 299 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00241 (18281) covalent geometry : angle 0.50369 (24792) SS BOND : bond 0.00146 ( 18) SS BOND : angle 1.37358 ( 36) hydrogen bonds : bond 0.04531 ( 760) hydrogen bonds : angle 3.82867 ( 2197) link_BETA1-4 : bond 0.00223 ( 3) link_BETA1-4 : angle 1.37367 ( 9) link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 1.63554 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.73 seconds wall clock time: 52 minutes 52.87 seconds (3172.87 seconds total)