Starting phenix.real_space_refine on Sat Jul 4 02:47:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szi_40917/07_2026/8szi_40917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szi_40917/07_2026/8szi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8szi_40917/07_2026/8szi_40917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szi_40917/07_2026/8szi_40917.map" model { file = "/net/cci-nas-00/data/ceres_data/8szi_40917/07_2026/8szi_40917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szi_40917/07_2026/8szi_40917.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 103 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1005 "'] Classifications: {'peptide': 2, 'undetermined': 3} Modifications used: {'COO': 2} Link IDs: {None: 3} Chain breaks: 2 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, 130 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1407 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain breaks: 2 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: 5.01, per 1000 atoms: 0.28 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: 1.32 Conformation dependent library (CDL) restraints added in 770.9 milliseconds 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: 0.68 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: 3.05 Time building geometry restraints manager: 1.70 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 3.250 nonbonded pdb=" O LEU B 88 " pdb="CA CA B1405 " model vdw 2.085 3.250 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: 10.060 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 are 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/Z covalent geometry : bond 0.00750 / 0.50 (18281) covalent geometry : angle 0.96560 / 0.65 (24792) SS BOND : bond 0.00824 / 0.56 ( 18) SS BOND : angle 1.76924 / 1.59 ( 36) hydrogen bonds : bond 0.21817 / 15.05 ( 760) hydrogen bonds : angle 6.30726 / 4.43 ( 2197) link_BETA1-4 : bond 0.00271 / 0.13 ( 3) link_BETA1-4 : angle 1.35610 / 0.83 ( 9) link_NAG-ASN : bond 0.00367 / 0.28 ( 6) link_NAG-ASN : angle 2.57753 / 1.80 ( 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 : 0.554 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: 0.1297 time to fit residues: 64.5616 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 : 0.670 ------------------------------------------------------------------------------- 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: 2.9990 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... 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 = 0.089271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074381 restraints weight = 73109.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076852 restraints weight = 118515.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077340 restraints weight = 47458.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077961 restraints weight = 39092.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078127 restraints weight = 33918.658| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- 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 = 0.30 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18308 Z= 0.157 Angle : 0.567 8.807 24855 Z= 0.303 Chirality : 0.044 0.193 2804 Planarity : 0.004 0.048 3121 Dihedral : 8.262 82.526 2751 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.65 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 are not related in a simple way. whole: 0.40 (0.18), residues: 2227 helix: 1.81 (0.18), residues: 879 sheet: -0.60 (0.26), residues: 398 loop : -0.78 (0.19), residues: 950 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 0.027 0.002 PHE A 789 TRP 0.031 0.002 TRP A 719 HIS 0.014 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (18281) covalent geometry : angle 0.56010 / 0.30 (24792) SS BOND : bond 0.00342 / 0.17 ( 18) SS BOND : angle 1.86372 / 1.26 ( 36) hydrogen bonds : bond 0.06768 / 4.47 ( 760) hydrogen bonds : angle 4.48429 / 3.17 ( 2197) link_BETA1-4 : bond 0.00285 / 0.14 ( 3) link_BETA1-4 : angle 1.75571 / 1.06 ( 9) link_NAG-ASN : bond 0.00242 / 0.12 ( 6) link_NAG-ASN : angle 1.77506 / 1.25 ( 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 243 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7730 (mtm180) REVERT: D 14 LEU cc_start: 0.7324 (mm) cc_final: 0.6905 (mp) REVERT: A 58 VAL cc_start: 0.8681 (p) cc_final: 0.8478 (m) REVERT: A 657 SER cc_start: 0.8681 (t) cc_final: 0.8422 (m) REVERT: A 663 SER cc_start: 0.8713 (t) cc_final: 0.8214 (p) REVERT: A 704 LEU cc_start: 0.8402 (tp) cc_final: 0.8089 (mt) REVERT: B 58 VAL cc_start: 0.8352 (p) cc_final: 0.8009 (m) REVERT: B 357 ASN cc_start: 0.8358 (t0) cc_final: 0.7947 (t0) REVERT: B 636 LYS cc_start: 0.6647 (mmtt) cc_final: 0.6419 (mmtt) REVERT: B 643 VAL cc_start: 0.7691 (m) cc_final: 0.7347 (t) REVERT: B 706 PHE cc_start: 0.6119 (t80) cc_final: 0.5749 (t80) REVERT: B 814 PHE cc_start: 0.8379 (t80) cc_final: 0.8171 (t80) outliers start: 20 outliers final: 10 residues processed: 236 average time/residue: 0.1284 time to fit residues: 44.9731 Evaluate side-chains 200 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 187 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 333 GLN D 175 GLN A 117 GLN A 193 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 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072752 restraints weight = 59491.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072895 restraints weight = 80978.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.073284 restraints weight = 78818.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074815 restraints weight = 49915.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075147 restraints weight = 35207.561| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18308 Z= 0.159 Angle : 0.547 7.326 24855 Z= 0.291 Chirality : 0.044 0.200 2804 Planarity : 0.004 0.049 3121 Dihedral : 7.642 74.982 2751 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.12 % Allowed : 8.99 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2227 helix: 1.74 (0.17), residues: 889 sheet: -0.60 (0.26), residues: 392 loop : -0.83 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 340 TYR 0.016 0.001 TYR B 421 PHE 0.018 0.002 PHE A 814 TRP 0.022 0.002 TRP A 719 HIS 0.014 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (18281) covalent geometry : angle 0.54122 / 0.29 (24792) SS BOND : bond 0.00236 / 0.16 ( 18) SS BOND : angle 1.50673 / 1.02 ( 36) hydrogen bonds : bond 0.05955 / 3.91 ( 760) hydrogen bonds : angle 4.23099 / 3.00 ( 2197) link_BETA1-4 : bond 0.00248 / 0.13 ( 3) link_BETA1-4 : angle 1.55692 / 0.94 ( 9) link_NAG-ASN : bond 0.00185 / 0.12 ( 6) link_NAG-ASN : angle 1.94296 / 1.39 ( 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 220 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.552 Fit side-chains REVERT: C 24 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7822 (mtm180) REVERT: D 181 THR cc_start: 0.8191 (p) cc_final: 0.7973 (t) REVERT: A 58 VAL cc_start: 0.8662 (p) cc_final: 0.8422 (m) REVERT: A 570 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6322 (t0) REVERT: A 657 SER cc_start: 0.8679 (t) cc_final: 0.8428 (m) REVERT: A 663 SER cc_start: 0.8719 (t) cc_final: 0.8220 (p) REVERT: A 704 LEU cc_start: 0.8521 (tp) cc_final: 0.8123 (mt) REVERT: A 789 PHE cc_start: 0.7421 (t80) cc_final: 0.6775 (t80) REVERT: B 643 VAL cc_start: 0.7566 (m) cc_final: 0.7284 (t) REVERT: B 688 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: B 706 PHE cc_start: 0.6277 (t80) cc_final: 0.5894 (t80) outliers start: 21 outliers final: 12 residues processed: 213 average time/residue: 0.1280 time to fit residues: 40.5297 Evaluate side-chains 202 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 597 SER 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 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: 0.7980 chunk 165 optimal weight: 0.3980 chunk 157 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 GLN D 175 GLN A 117 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 463 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073451 restraints weight = 66866.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.075522 restraints weight = 106601.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075872 restraints weight = 61382.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076234 restraints weight = 43414.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078428 restraints weight = 39099.575| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 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 = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18308 Z= 0.119 Angle : 0.499 8.124 24855 Z= 0.266 Chirality : 0.042 0.174 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.220 70.077 2751 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.28 % Allowed : 10.17 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2227 helix: 2.00 (0.17), residues: 882 sheet: -0.56 (0.26), residues: 392 loop : -0.85 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.014 0.001 TYR B 421 PHE 0.016 0.001 PHE B 629 TRP 0.022 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (18281) covalent geometry : angle 0.49295 / 0.26 (24792) SS BOND : bond 0.00170 / 0.12 ( 18) SS BOND : angle 1.48925 / 1.02 ( 36) hydrogen bonds : bond 0.05018 / 3.29 ( 760) hydrogen bonds : angle 3.99551 / 2.83 ( 2197) link_BETA1-4 : bond 0.00257 / 0.12 ( 3) link_BETA1-4 : angle 1.46676 / 0.88 ( 9) link_NAG-ASN : bond 0.00163 / 0.09 ( 6) link_NAG-ASN : angle 1.74385 / 1.23 ( 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 215 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.441 Fit side-chains REVERT: C 24 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7801 (mtm180) REVERT: D 181 THR cc_start: 0.8078 (p) cc_final: 0.7870 (t) REVERT: D 297 TRP cc_start: 0.8307 (m100) cc_final: 0.8100 (m100) REVERT: A 58 VAL cc_start: 0.8652 (p) cc_final: 0.8437 (m) REVERT: A 570 ASP cc_start: 0.6415 (OUTLIER) cc_final: 0.6197 (t0) REVERT: A 657 SER cc_start: 0.8699 (t) cc_final: 0.8453 (m) REVERT: A 663 SER cc_start: 0.8701 (t) cc_final: 0.8209 (p) REVERT: B 270 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 688 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7084 (m-80) outliers start: 24 outliers final: 13 residues processed: 207 average time/residue: 0.1253 time to fit residues: 39.6825 Evaluate side-chains 198 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL 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 270 PHE 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: 3.9990 chunk 193 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 69 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3505 r_free = 0.3505 target = 0.088692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073028 restraints weight = 60504.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073098 restraints weight = 78777.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073826 restraints weight = 58920.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074537 restraints weight = 44584.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074793 restraints weight = 42342.085| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18308 Z= 0.140 Angle : 0.517 8.002 24855 Z= 0.275 Chirality : 0.043 0.273 2804 Planarity : 0.004 0.050 3121 Dihedral : 6.993 66.086 2751 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.44 % Allowed : 10.97 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2227 helix: 1.97 (0.17), residues: 882 sheet: -0.64 (0.26), residues: 388 loop : -0.87 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 340 TYR 0.015 0.001 TYR B 421 PHE 0.030 0.001 PHE A 789 TRP 0.016 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18281) covalent geometry : angle 0.51136 / 0.27 (24792) SS BOND : bond 0.00178 / 0.14 ( 18) SS BOND : angle 1.51464 / 1.02 ( 36) hydrogen bonds : bond 0.05212 / 3.41 ( 760) hydrogen bonds : angle 3.97729 / 2.82 ( 2197) link_BETA1-4 : bond 0.00220 / 0.11 ( 3) link_BETA1-4 : angle 1.51569 / 0.92 ( 9) link_NAG-ASN : bond 0.00150 / 0.08 ( 6) link_NAG-ASN : angle 1.75374 / 1.25 ( 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: 27 poor density : 191 time to evaluate : 0.593 Fit side-chains REVERT: C 24 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7815 (mtm180) REVERT: C 29 LYS cc_start: 0.8422 (tptt) cc_final: 0.7875 (ttpp) REVERT: A 58 VAL cc_start: 0.8618 (p) cc_final: 0.8409 (m) REVERT: A 570 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6362 (t0) REVERT: A 657 SER cc_start: 0.8672 (t) cc_final: 0.8421 (m) REVERT: A 663 SER cc_start: 0.8717 (t) cc_final: 0.8202 (p) REVERT: B 270 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8202 (t80) REVERT: B 688 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7139 (m-80) outliers start: 27 outliers final: 20 residues processed: 208 average time/residue: 0.1324 time to fit residues: 41.8109 Evaluate side-chains 209 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 101 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3518 r_free = 0.3518 target = 0.089266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072484 restraints weight = 51001.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072295 restraints weight = 54333.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072798 restraints weight = 52992.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.072924 restraints weight = 40088.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073013 restraints weight = 43411.742| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 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 = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18308 Z= 0.111 Angle : 0.493 7.920 24855 Z= 0.262 Chirality : 0.041 0.214 2804 Planarity : 0.004 0.047 3121 Dihedral : 6.782 64.506 2751 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.50 % Allowed : 11.82 % 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 are not related in a simple way. whole: 0.57 (0.18), residues: 2227 helix: 2.10 (0.17), residues: 881 sheet: -0.56 (0.26), residues: 382 loop : -0.83 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 340 TYR 0.014 0.001 TYR B 421 PHE 0.025 0.001 PHE A 733 TRP 0.014 0.001 TRP A 299 HIS 0.013 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18281) covalent geometry : angle 0.48771 / 0.26 (24792) SS BOND : bond 0.00151 / 0.11 ( 18) SS BOND : angle 1.41585 / 0.96 ( 36) hydrogen bonds : bond 0.04728 / 3.09 ( 760) hydrogen bonds : angle 3.86882 / 2.75 ( 2197) link_BETA1-4 : bond 0.00215 / 0.10 ( 3) link_BETA1-4 : angle 1.40401 / 0.84 ( 9) link_NAG-ASN : bond 0.00151 / 0.07 ( 6) link_NAG-ASN : angle 1.68507 / 1.19 ( 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 214 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7805 (mtm180) REVERT: C 29 LYS cc_start: 0.8353 (tptt) cc_final: 0.7848 (ttpp) REVERT: A 570 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6380 (t0) REVERT: A 657 SER cc_start: 0.8666 (t) cc_final: 0.8425 (m) REVERT: A 663 SER cc_start: 0.8695 (t) cc_final: 0.8188 (p) REVERT: B 270 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8248 (t80) REVERT: B 688 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: B 818 TRP cc_start: 0.8430 (m100) cc_final: 0.8181 (m100) outliers start: 28 outliers final: 18 residues processed: 206 average time/residue: 0.1272 time to fit residues: 39.5534 Evaluate side-chains 200 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 208 optimal weight: 0.5980 chunk 199 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 2 optimal weight: 0.0170 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3523 r_free = 0.3523 target = 0.089533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074708 restraints weight = 78408.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076888 restraints weight = 124051.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077917 restraints weight = 48009.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078821 restraints weight = 36204.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079009 restraints weight = 27697.038| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2579 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= 0.108 Angle : 0.492 7.896 24855 Z= 0.259 Chirality : 0.041 0.195 2804 Planarity : 0.004 0.061 3121 Dihedral : 6.589 62.190 2751 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.44 % Allowed : 12.36 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2227 helix: 2.16 (0.17), residues: 881 sheet: -0.52 (0.26), residues: 382 loop : -0.82 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 340 TYR 0.013 0.001 TYR B 421 PHE 0.033 0.001 PHE A 789 TRP 0.022 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18281) covalent geometry : angle 0.48765 / 0.26 (24792) SS BOND : bond 0.00140 / 0.11 ( 18) SS BOND : angle 1.38065 / 0.93 ( 36) hydrogen bonds : bond 0.04490 / 2.94 ( 760) hydrogen bonds : angle 3.79730 / 2.70 ( 2197) link_BETA1-4 : bond 0.00273 / 0.13 ( 3) link_BETA1-4 : angle 1.35789 / 0.81 ( 9) link_NAG-ASN : bond 0.00143 / 0.07 ( 6) link_NAG-ASN : angle 1.56602 / 1.11 ( 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 214 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7794 (mtm180) REVERT: C 29 LYS cc_start: 0.8221 (tptt) cc_final: 0.7817 (ttpp) REVERT: C 290 TYR cc_start: 0.6462 (p90) cc_final: 0.6191 (p90) REVERT: D 297 TRP cc_start: 0.8296 (m100) cc_final: 0.8045 (m100) REVERT: A 570 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.6296 (t0) REVERT: A 657 SER cc_start: 0.8681 (t) cc_final: 0.8415 (m) REVERT: A 663 SER cc_start: 0.8668 (t) cc_final: 0.8206 (p) REVERT: B 270 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8256 (t80) REVERT: B 688 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: B 818 TRP cc_start: 0.8433 (m100) cc_final: 0.8116 (m100) REVERT: B 819 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8177 (tp) outliers start: 27 outliers final: 21 residues processed: 207 average time/residue: 0.1307 time to fit residues: 41.0154 Evaluate side-chains 209 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 123 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071952 restraints weight = 75105.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074648 restraints weight = 117101.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075289 restraints weight = 48661.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076546 restraints weight = 38332.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076633 restraints weight = 30493.792| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18308 Z= 0.171 Angle : 0.548 8.601 24855 Z= 0.291 Chirality : 0.043 0.208 2804 Planarity : 0.004 0.050 3121 Dihedral : 6.725 60.398 2751 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.50 % Allowed : 13.00 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2227 helix: 1.90 (0.17), residues: 888 sheet: -0.58 (0.26), residues: 386 loop : -0.90 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 340 TYR 0.017 0.002 TYR B 421 PHE 0.024 0.002 PHE B 729 TRP 0.015 0.002 TRP A 719 HIS 0.021 0.002 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (18281) covalent geometry : angle 0.54226 / 0.29 (24792) SS BOND : bond 0.00218 / 0.17 ( 18) SS BOND : angle 1.54403 / 1.05 ( 36) hydrogen bonds : bond 0.05462 / 3.57 ( 760) hydrogen bonds : angle 3.97612 / 2.83 ( 2197) link_BETA1-4 : bond 0.00238 / 0.12 ( 3) link_BETA1-4 : angle 1.57390 / 0.96 ( 9) link_NAG-ASN : bond 0.00172 / 0.10 ( 6) link_NAG-ASN : angle 1.77727 / 1.29 ( 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 216 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8071 (mtm180) cc_final: 0.7866 (mtm180) REVERT: C 29 LYS cc_start: 0.8317 (tptt) cc_final: 0.7921 (ttpp) REVERT: A 570 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6386 (t0) REVERT: A 657 SER cc_start: 0.8663 (t) cc_final: 0.8414 (m) REVERT: A 663 SER cc_start: 0.8701 (t) cc_final: 0.8214 (p) REVERT: B 270 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8230 (t80) REVERT: B 688 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: B 818 TRP cc_start: 0.8459 (m100) cc_final: 0.8154 (m100) outliers start: 28 outliers final: 22 residues processed: 206 average time/residue: 0.1305 time to fit residues: 40.3238 Evaluate side-chains 209 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 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 = 0.3480 r_free = 0.3480 target = 0.087434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070863 restraints weight = 55008.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070554 restraints weight = 64668.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.071262 restraints weight = 52531.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071383 restraints weight = 41905.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071682 restraints weight = 42708.716| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 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 = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18308 Z= 0.203 Angle : 0.579 8.598 24855 Z= 0.307 Chirality : 0.045 0.216 2804 Planarity : 0.004 0.081 3121 Dihedral : 6.885 60.436 2751 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.50 % Allowed : 12.89 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2227 helix: 1.71 (0.17), residues: 894 sheet: -0.69 (0.26), residues: 388 loop : -0.97 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 340 TYR 0.019 0.002 TYR B 421 PHE 0.031 0.002 PHE A 733 TRP 0.015 0.002 TRP A 719 HIS 0.012 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 (18281) covalent geometry : angle 0.57353 / 0.31 (24792) SS BOND : bond 0.00267 / 0.20 ( 18) SS BOND : angle 1.63660 / 1.13 ( 36) hydrogen bonds : bond 0.05931 / 3.87 ( 760) hydrogen bonds : angle 4.08719 / 2.91 ( 2197) link_BETA1-4 : bond 0.00189 / 0.09 ( 3) link_BETA1-4 : angle 1.69595 / 1.05 ( 9) link_NAG-ASN : bond 0.00208 / 0.12 ( 6) link_NAG-ASN : angle 1.96293 / 1.44 ( 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 218 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8417 (tptt) cc_final: 0.8007 (ttpp) REVERT: C 230 TYR cc_start: 0.7555 (p90) cc_final: 0.7191 (p90) REVERT: A 570 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6566 (t0) REVERT: A 657 SER cc_start: 0.8604 (t) cc_final: 0.8375 (m) REVERT: A 663 SER cc_start: 0.8707 (t) cc_final: 0.8184 (p) REVERT: B 197 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: B 270 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 688 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7209 (m-80) outliers start: 28 outliers final: 20 residues processed: 210 average time/residue: 0.1219 time to fit residues: 38.4019 Evaluate side-chains 209 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 232 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 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 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: 0.9990 chunk 126 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 136 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.071135 restraints weight = 54611.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070534 restraints weight = 53733.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071171 restraints weight = 48489.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.071485 restraints weight = 36257.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071701 restraints weight = 34532.352| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 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 = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2691 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= 0.110 Angle : 0.503 7.932 24855 Z= 0.267 Chirality : 0.042 0.189 2804 Planarity : 0.004 0.047 3121 Dihedral : 6.585 58.689 2751 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.07 % Allowed : 13.59 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2227 helix: 2.06 (0.17), residues: 881 sheet: -0.55 (0.26), residues: 384 loop : -0.90 (0.19), residues: 962 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 0.023 0.001 PHE B 814 TRP 0.034 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18281) covalent geometry : angle 0.49729 / 0.27 (24792) SS BOND : bond 0.00160 / 0.12 ( 18) SS BOND : angle 1.40015 / 0.96 ( 36) hydrogen bonds : bond 0.04675 / 3.06 ( 760) hydrogen bonds : angle 3.87507 / 2.76 ( 2197) link_BETA1-4 : bond 0.00249 / 0.13 ( 3) link_BETA1-4 : angle 1.44393 / 0.87 ( 9) link_NAG-ASN : bond 0.00158 / 0.07 ( 6) link_NAG-ASN : angle 1.75858 / 1.25 ( 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 203 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8399 (tptt) cc_final: 0.7970 (ttpp) REVERT: D 14 LEU cc_start: 0.7610 (mm) cc_final: 0.7189 (mp) REVERT: A 570 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6471 (t0) REVERT: A 657 SER cc_start: 0.8666 (t) cc_final: 0.8424 (m) REVERT: A 663 SER cc_start: 0.8718 (t) cc_final: 0.8171 (p) REVERT: B 197 MET cc_start: 0.8289 (mtm) cc_final: 0.8038 (mtm) REVERT: B 270 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8347 (t80) REVERT: B 688 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7179 (m-80) outliers start: 20 outliers final: 13 residues processed: 198 average time/residue: 0.1274 time to fit residues: 37.2990 Evaluate side-chains 199 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 232 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 448 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 463 HIS 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 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: 2.9990 chunk 175 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 89 optimal weight: 0.0050 chunk 177 optimal weight: 1.9990 chunk 195 optimal weight: 0.0050 chunk 123 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 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 = 0.3532 r_free = 0.3532 target = 0.089977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072914 restraints weight = 55958.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073103 restraints weight = 47561.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073587 restraints weight = 40855.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073841 restraints weight = 33492.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074137 restraints weight = 32396.782| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 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 = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18308 Z= 0.099 Angle : 0.496 15.172 24855 Z= 0.262 Chirality : 0.041 0.229 2804 Planarity : 0.004 0.081 3121 Dihedral : 6.246 57.936 2751 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.91 % Allowed : 13.54 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2227 helix: 2.29 (0.17), residues: 869 sheet: -0.52 (0.27), residues: 379 loop : -0.77 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 340 TYR 0.011 0.001 TYR B 421 PHE 0.038 0.001 PHE A 733 TRP 0.030 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (18281) covalent geometry : angle 0.49183 / 0.26 (24792) SS BOND : bond 0.00135 / 0.10 ( 18) SS BOND : angle 1.32077 / 0.90 ( 36) hydrogen bonds : bond 0.04096 / 2.69 ( 760) hydrogen bonds : angle 3.74051 / 2.67 ( 2197) link_BETA1-4 : bond 0.00277 / 0.13 ( 3) link_BETA1-4 : angle 1.27264 / 0.76 ( 9) link_NAG-ASN : bond 0.00183 / 0.09 ( 6) link_NAG-ASN : angle 1.49540 / 1.06 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.85 seconds wall clock time: 48 minutes 5.16 seconds (2885.16 seconds total)