Starting phenix.real_space_refine on Sun Sep 29 18:55:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om7_16970/09_2024/8om7_16970_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om7_16970/09_2024/8om7_16970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om7_16970/09_2024/8om7_16970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om7_16970/09_2024/8om7_16970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om7_16970/09_2024/8om7_16970_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om7_16970/09_2024/8om7_16970_trim.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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 P 12 5.49 5 S 162 5.16 5 C 23418 2.51 5 N 6426 2.21 5 O 6972 1.98 5 H 37686 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74676 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12419 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 12419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12419 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 12419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12419 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 12419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12419 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 12419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12419 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 12419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12419 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.16, per 1000 atoms: 0.35 Number of scatterers: 74676 At special positions: 0 Unit cell: (150.336, 147.204, 222.372, 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) S 162 16.00 P 12 15.00 O 6972 8.00 N 6426 7.00 C 23418 6.00 H 37686 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM74617 O3A ADP D1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.30 Conformation dependent library (CDL) restraints added in 4.5 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 38 sheets defined 52.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.992A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.748A pdb=" N VAL A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.563A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.642A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.539A pdb=" N GLU A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 408 removed outlier: 4.669A pdb=" N GLU A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.779A pdb=" N LYS A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.508A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.573A pdb=" N LYS A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.161A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.608A pdb=" N GLN A 743 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 849 through 855 Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 938 through 947 removed outlier: 4.179A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.713A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.741A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.951A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.634A pdb=" N GLU B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 389 Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.934A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 428 removed outlier: 4.264A pdb=" N GLU B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.556A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.663A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 602 through 612 removed outlier: 4.119A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.035A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.557A pdb=" N THR B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 914 through 922 removed outlier: 3.985A pdb=" N LYS B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 929 removed outlier: 5.902A pdb=" N PHE B 926 " --> pdb=" O LEU B 923 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 4.208A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 157 removed outlier: 3.612A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.701A pdb=" N VAL C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.809A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.523A pdb=" N GLN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.537A pdb=" N LEU C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 removed outlier: 3.549A pdb=" N GLU C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 404 Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.868A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.538A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.709A pdb=" N ALA C 483 " --> pdb=" O ASP C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 530 through 541 removed outlier: 3.770A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 612 removed outlier: 4.323A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.819A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 738 through 746 removed outlier: 3.729A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 852 through 855 Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 924 through 928 Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.285A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 157 removed outlier: 3.845A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 removed outlier: 3.749A pdb=" N VAL D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 307 removed outlier: 3.714A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 removed outlier: 3.802A pdb=" N MET D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.634A pdb=" N LEU D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 354 through 389 Processing helix chain 'D' and resid 391 through 403 removed outlier: 4.022A pdb=" N LEU D 395 " --> pdb=" O HIS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 428 removed outlier: 3.721A pdb=" N ARG D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.578A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 removed outlier: 3.685A pdb=" N ALA D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 511 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.556A pdb=" N GLN D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 603 through 612 Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 646 through 651 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 738 through 747 removed outlier: 3.837A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 745 " --> pdb=" O ASN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 852 through 855 Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 906 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 923 through 928 removed outlier: 5.917A pdb=" N PHE D 926 " --> pdb=" O LEU D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.141A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.660A pdb=" N GLU E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.818A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 307 removed outlier: 3.892A pdb=" N LEU E 292 " --> pdb=" O GLU E 288 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.508A pdb=" N LEU E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 352 removed outlier: 3.539A pdb=" N GLU E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 389 Processing helix chain 'E' and resid 391 through 403 removed outlier: 3.774A pdb=" N LEU E 395 " --> pdb=" O HIS E 391 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 427 removed outlier: 4.075A pdb=" N LYS E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.574A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 removed outlier: 3.656A pdb=" N ALA E 483 " --> pdb=" O ASP E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.482A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 646 through 653 removed outlier: 3.717A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET E 653 " --> pdb=" O LEU E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 730 Processing helix chain 'E' and resid 738 through 746 removed outlier: 3.712A pdb=" N GLN E 743 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE E 745 " --> pdb=" O ASN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 756 removed outlier: 4.503A pdb=" N MET E 756 " --> pdb=" O VAL E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 849 through 855 Proline residue: E 854 - end of helix Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 906 removed outlier: 3.545A pdb=" N LYS E 898 " --> pdb=" O GLY E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 924 through 928 Processing helix chain 'E' and resid 938 through 947 removed outlier: 4.206A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE E 947 " --> pdb=" O PHE E 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 removed outlier: 3.917A pdb=" N GLU F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 290 through 307 removed outlier: 3.848A pdb=" N ALA F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 319 through 323 removed outlier: 4.051A pdb=" N ARG F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.794A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.529A pdb=" N GLU F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 407 removed outlier: 3.548A pdb=" N LEU F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 428 removed outlier: 4.222A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.664A pdb=" N ILE F 468 " --> pdb=" O TRP F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 491 removed outlier: 3.737A pdb=" N ALA F 483 " --> pdb=" O ASP F 479 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS F 491 " --> pdb=" O LEU F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 541 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 592 through 595 Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.380A pdb=" N ALA F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.554A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 747 removed outlier: 3.742A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 849 through 855 Proline residue: F 854 - end of helix Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 906 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 924 through 928 Processing helix chain 'F' and resid 938 through 947 removed outlier: 4.513A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.428A pdb=" N LEU A 168 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 188 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 544 through 548 Processing sheet with id=AA4, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.733A pdb=" N LYS A 690 " --> pdb=" O VAL A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.877A pdb=" N LEU A 842 " --> pdb=" O GLU A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 877 through 879 removed outlier: 7.026A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 169 removed outlier: 6.805A pdb=" N VAL B 164 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 190 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 166 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 188 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU B 168 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.371A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.460A pdb=" N LYS B 690 " --> pdb=" O VAL B 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 764 through 769 removed outlier: 3.544A pdb=" N THR B 803 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.250A pdb=" N ILE B 910 " --> pdb=" O HIS B 934 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL B 936 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 912 " --> pdb=" O VAL B 936 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.169A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 689 through 691 Processing sheet with id=AB8, first strand: chain 'C' and resid 764 through 769 removed outlier: 4.030A pdb=" N LEU C 842 " --> pdb=" O GLU C 801 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 877 through 879 removed outlier: 7.129A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.852A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC3, first strand: chain 'D' and resid 164 through 167 Processing sheet with id=AC4, first strand: chain 'D' and resid 519 through 522 removed outlier: 7.033A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 689 through 691 Processing sheet with id=AC6, first strand: chain 'D' and resid 764 through 769 removed outlier: 6.618A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 877 through 879 removed outlier: 6.332A pdb=" N ILE D 910 " --> pdb=" O HIS D 934 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 936 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC9, first strand: chain 'E' and resid 164 through 167 Processing sheet with id=AD1, first strand: chain 'E' and resid 636 through 639 removed outlier: 5.809A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 544 through 548 Processing sheet with id=AD3, first strand: chain 'E' and resid 689 through 691 removed outlier: 3.827A pdb=" N VAL E 737 " --> pdb=" O LYS E 690 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 764 through 769 removed outlier: 3.869A pdb=" N LEU E 842 " --> pdb=" O GLU E 801 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 877 through 879 Processing sheet with id=AD6, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AD7, first strand: chain 'F' and resid 163 through 169 removed outlier: 4.414A pdb=" N LEU F 168 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR F 188 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 544 through 548 removed outlier: 3.585A pdb=" N CYS F 637 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 690 through 691 removed outlier: 6.420A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 764 through 769 removed outlier: 3.511A pdb=" N GLU F 801 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 842 " --> pdb=" O GLU F 801 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.561A pdb=" N ILE F 910 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL F 936 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU F 912 " --> pdb=" O VAL F 936 " (cutoff:3.500A) 1773 hydrogen bonds defined for protein. 5043 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: 28.31 Time building geometry restraints manager: 18.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 37644 1.04 - 1.23: 586 1.23 - 1.43: 14385 1.43 - 1.63: 22397 1.63 - 1.82: 282 Bond restraints: 75294 Sorted by residual: bond pdb=" N HIS C 123 " pdb=" CA HIS C 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N HIS A 123 " pdb=" CA HIS A 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N HIS E 123 " pdb=" CA HIS E 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N HIS D 123 " pdb=" CA HIS D 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N HIS F 123 " pdb=" CA HIS F 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 75289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 136831 7.10 - 14.19: 4 14.19 - 21.29: 0 21.29 - 28.38: 5 28.38 - 35.48: 8 Bond angle restraints: 136848 Sorted by residual: angle pdb=" C LYS D 404 " pdb=" CA LYS D 404 " pdb=" HA LYS D 404 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C ASP D 758 " pdb=" CA ASP D 758 " pdb=" HA ASP D 758 " ideal model delta sigma weight residual 109.00 73.67 35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N ASP D 758 " pdb=" CA ASP D 758 " pdb=" HA ASP D 758 " ideal model delta sigma weight residual 110.00 75.26 34.74 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LYS D 404 " pdb=" CA LYS D 404 " pdb=" HA LYS D 404 " ideal model delta sigma weight residual 110.00 75.77 34.23 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB LYS D 404 " pdb=" CA LYS D 404 " pdb=" HA LYS D 404 " ideal model delta sigma weight residual 109.00 75.02 33.98 3.00e+00 1.11e-01 1.28e+02 ... (remaining 136843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 33859 35.42 - 70.83: 976 70.83 - 106.25: 39 106.25 - 141.66: 4 141.66 - 177.08: 6 Dihedral angle restraints: 34884 sinusoidal: 19674 harmonic: 15210 Sorted by residual: dihedral pdb=" C5' ADP D1001 " pdb=" O5' ADP D1001 " pdb=" PA ADP D1001 " pdb=" O2A ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 117.08 -177.08 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PB ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 116.49 -176.50 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2' ADP B1001 " pdb=" C1' ADP B1001 " pdb=" N9 ADP B1001 " pdb=" C4 ADP B1001 " ideal model delta sinusoidal sigma weight residual 91.55 -103.29 -165.17 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 34881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5406 0.079 - 0.157: 424 0.157 - 0.236: 0 0.236 - 0.314: 0 0.314 - 0.393: 2 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CA ASP D 758 " pdb=" N ASP D 758 " pdb=" C ASP D 758 " pdb=" CB ASP D 758 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA LYS D 404 " pdb=" N LYS D 404 " pdb=" C LYS D 404 " pdb=" CB LYS D 404 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 5829 not shown) Planarity restraints: 10974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 748 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 749 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 749 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 749 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 600 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLN D 600 " 0.030 2.00e-02 2.50e+03 pdb=" O GLN D 600 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 601 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 430 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO F 431 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 431 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 431 " -0.024 5.00e-02 4.00e+02 ... (remaining 10971 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 2722 2.15 - 2.76: 145287 2.76 - 3.37: 211732 3.37 - 3.99: 256898 3.99 - 4.60: 400868 Nonbonded interactions: 1017507 Sorted by model distance: nonbonded pdb=" O PRO A 787 " pdb=" HZ3 LYS A 790 " model vdw 1.534 2.450 nonbonded pdb=" OE1 GLN B 788 " pdb=" H GLN B 788 " model vdw 1.535 2.450 nonbonded pdb=" O PRO D 787 " pdb=" HZ3 LYS D 790 " model vdw 1.540 2.450 nonbonded pdb=" OE1 GLU C 740 " pdb=" H GLU C 740 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLU C 937 " pdb=" H GLU C 937 " model vdw 1.556 2.450 ... (remaining 1017502 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.970 Extract box with map and model: 2.050 Check model and map are aligned: 0.430 Set scattering table: 0.520 Process input model: 122.260 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.320 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: 0.040 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.002 0.046 37608 Z= 0.157 Angle : 0.568 24.366 50802 Z= 0.293 Chirality : 0.038 0.393 5832 Planarity : 0.003 0.053 6522 Dihedral : 15.472 177.079 14460 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.02 % Allowed : 15.43 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4632 helix: 1.35 (0.12), residues: 2104 sheet: -2.00 (0.22), residues: 549 loop : -0.81 (0.15), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 464 HIS 0.005 0.001 HIS D 491 PHE 0.014 0.001 PHE B 779 TYR 0.010 0.001 TYR E 939 ARG 0.004 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.6415 (tttt) cc_final: 0.6190 (tttp) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 1.0673 time to fit residues: 278.7602 Evaluate side-chains 162 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 751 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 8.9990 chunk 350 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A 640 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 37608 Z= 0.392 Angle : 0.659 9.994 50802 Z= 0.347 Chirality : 0.041 0.421 5832 Planarity : 0.005 0.065 6522 Dihedral : 8.331 177.313 5120 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.28 % Allowed : 15.80 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4632 helix: 1.00 (0.11), residues: 2169 sheet: -2.06 (0.22), residues: 535 loop : -1.28 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 464 HIS 0.007 0.001 HIS D 491 PHE 0.022 0.002 PHE B 820 TYR 0.012 0.002 TYR A 757 ARG 0.007 0.001 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 729 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7324 (p) REVERT: D 786 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8316 (ttp80) REVERT: F 879 MET cc_start: 0.6222 (ptp) cc_final: 0.6006 (ptp) outliers start: 52 outliers final: 29 residues processed: 205 average time/residue: 1.0317 time to fit residues: 345.5487 Evaluate side-chains 188 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 753 VAL Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 866 SER Chi-restraints excluded: chain F residue 896 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 454 optimal weight: 0.5980 chunk 374 optimal weight: 8.9990 chunk 416 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 219 GLN ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 37608 Z= 0.289 Angle : 0.591 7.252 50802 Z= 0.306 Chirality : 0.040 0.393 5832 Planarity : 0.004 0.067 6522 Dihedral : 7.943 163.175 5120 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.43 % Allowed : 16.67 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4632 helix: 1.07 (0.11), residues: 2162 sheet: -2.16 (0.22), residues: 545 loop : -1.44 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 464 HIS 0.006 0.001 HIS D 491 PHE 0.017 0.001 PHE B 820 TYR 0.014 0.001 TYR F 939 ARG 0.005 0.000 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.6932 (tttm) cc_final: 0.6531 (ptmt) REVERT: C 875 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: D 552 MET cc_start: 0.6951 (tpt) cc_final: 0.6744 (tpt) REVERT: D 786 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8339 (ttp80) REVERT: F 879 MET cc_start: 0.6707 (ptp) cc_final: 0.6393 (ptp) outliers start: 58 outliers final: 42 residues processed: 214 average time/residue: 1.0141 time to fit residues: 352.9200 Evaluate side-chains 201 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 563 ARG Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 844 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 282 optimal weight: 7.9990 chunk 421 optimal weight: 7.9990 chunk 446 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 399 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 657 ASN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37608 Z= 0.275 Angle : 0.577 6.954 50802 Z= 0.298 Chirality : 0.040 0.407 5832 Planarity : 0.004 0.066 6522 Dihedral : 7.776 164.876 5120 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.90 % Allowed : 16.74 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4632 helix: 1.11 (0.11), residues: 2175 sheet: -2.21 (0.21), residues: 556 loop : -1.43 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 464 HIS 0.007 0.001 HIS D 491 PHE 0.020 0.001 PHE B 820 TYR 0.013 0.001 TYR F 939 ARG 0.005 0.000 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 157 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.6971 (tttm) cc_final: 0.6635 (ptmt) REVERT: C 875 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: D 552 MET cc_start: 0.7172 (tpt) cc_final: 0.6968 (tpt) REVERT: D 651 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8247 (p0) REVERT: D 786 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8269 (ttp80) REVERT: F 879 MET cc_start: 0.6756 (ptp) cc_final: 0.6432 (ptp) outliers start: 77 outliers final: 60 residues processed: 225 average time/residue: 0.9935 time to fit residues: 363.3736 Evaluate side-chains 218 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 155 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain D residue 941 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 563 ARG Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 786 ARG Chi-restraints excluded: chain F residue 844 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 7.9990 chunk 253 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 381 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 400 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN C 219 GLN C 640 ASN E 657 ASN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 37608 Z= 0.368 Angle : 0.652 9.860 50802 Z= 0.341 Chirality : 0.041 0.400 5832 Planarity : 0.005 0.070 6522 Dihedral : 7.763 166.727 5120 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.69 % Allowed : 17.53 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4632 helix: 0.67 (0.11), residues: 2168 sheet: -2.28 (0.21), residues: 554 loop : -1.73 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 464 HIS 0.009 0.002 HIS D 491 PHE 0.028 0.002 PHE B 820 TYR 0.016 0.002 TYR F 565 ARG 0.007 0.001 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 156 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ASP cc_start: -0.1578 (OUTLIER) cc_final: -0.2258 (p0) REVERT: A 748 LYS cc_start: 0.7044 (tttm) cc_final: 0.6690 (ptmt) REVERT: C 875 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: C 937 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: D 597 ARG cc_start: 0.7020 (ptm-80) cc_final: 0.6601 (ptm-80) outliers start: 109 outliers final: 79 residues processed: 256 average time/residue: 0.9813 time to fit residues: 412.5104 Evaluate side-chains 235 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 153 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 754 GLU Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 849 THR Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain D residue 941 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 562 ARG Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 643 ASP Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 786 ARG Chi-restraints excluded: chain F residue 790 LYS Chi-restraints excluded: chain F residue 844 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 0.4980 chunk 402 optimal weight: 4.9990 chunk 88 optimal weight: 0.0060 chunk 262 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 447 optimal weight: 2.9990 chunk 371 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 875 GLN C 219 GLN D 839 HIS E 509 GLN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37608 Z= 0.179 Angle : 0.549 8.350 50802 Z= 0.279 Chirality : 0.040 0.391 5832 Planarity : 0.004 0.087 6522 Dihedral : 7.534 166.321 5120 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.56 % Allowed : 18.30 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 4632 helix: 1.20 (0.11), residues: 2172 sheet: -2.14 (0.22), residues: 550 loop : -1.55 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 464 HIS 0.007 0.001 HIS A 491 PHE 0.017 0.001 PHE C 820 TYR 0.017 0.001 TYR F 939 ARG 0.011 0.000 ARG E 563 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 937 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: D 651 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8279 (p0) REVERT: E 653 MET cc_start: 0.6501 (pmm) cc_final: 0.6104 (pmm) REVERT: F 786 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7457 (ttp80) outliers start: 63 outliers final: 46 residues processed: 217 average time/residue: 0.9895 time to fit residues: 347.9907 Evaluate side-chains 204 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 786 ARG Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 376 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 445 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 460 ASN E 509 GLN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37608 Z= 0.282 Angle : 0.587 8.333 50802 Z= 0.302 Chirality : 0.040 0.401 5832 Planarity : 0.004 0.064 6522 Dihedral : 7.400 166.124 5120 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.80 % Allowed : 18.72 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4632 helix: 1.08 (0.11), residues: 2175 sheet: -2.16 (0.21), residues: 567 loop : -1.60 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 464 HIS 0.006 0.001 HIS D 491 PHE 0.030 0.002 PHE B 619 TYR 0.018 0.001 TYR F 939 ARG 0.008 0.000 ARG E 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 155 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 875 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: C 937 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: D 651 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8195 (p0) outliers start: 73 outliers final: 63 residues processed: 222 average time/residue: 0.9513 time to fit residues: 346.8763 Evaluate side-chains 216 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 150 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 727 ILE Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain C residue 940 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain D residue 941 GLU Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 350 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 509 GLN F 187 HIS F 515 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37608 Z= 0.214 Angle : 0.553 7.785 50802 Z= 0.281 Chirality : 0.039 0.390 5832 Planarity : 0.004 0.061 6522 Dihedral : 7.300 165.913 5120 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.65 % Allowed : 18.84 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 4632 helix: 1.23 (0.11), residues: 2176 sheet: -2.06 (0.22), residues: 546 loop : -1.59 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 464 HIS 0.006 0.001 HIS A 491 PHE 0.022 0.001 PHE B 619 TYR 0.015 0.001 TYR F 939 ARG 0.007 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 154 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 937 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: D 651 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8297 (p0) outliers start: 67 outliers final: 62 residues processed: 214 average time/residue: 0.9493 time to fit residues: 333.5543 Evaluate side-chains 217 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 153 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 727 ILE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain C residue 940 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 10.0000 chunk 426 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 127 optimal weight: 0.0050 chunk 374 optimal weight: 9.9990 chunk 392 optimal weight: 6.9990 chunk 413 optimal weight: 20.0000 overall best weight: 7.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 219 GLN A 450 ASN ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN C 219 GLN C 460 ASN ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 HIS ** F 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 37608 Z= 0.525 Angle : 0.774 9.191 50802 Z= 0.413 Chirality : 0.044 0.417 5832 Planarity : 0.006 0.060 6522 Dihedral : 7.694 170.184 5120 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.52 % Allowed : 18.62 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.12), residues: 4632 helix: 0.13 (0.11), residues: 2174 sheet: -2.35 (0.21), residues: 560 loop : -2.07 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 770 HIS 0.010 0.002 HIS F 491 PHE 0.044 0.003 PHE B 820 TYR 0.020 0.002 TYR F 565 ARG 0.014 0.001 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 148 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6829 (mp) REVERT: A 790 LYS cc_start: 0.4578 (OUTLIER) cc_final: 0.3713 (tppt) REVERT: C 460 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7824 (m110) REVERT: C 875 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: C 937 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7615 (pm20) outliers start: 102 outliers final: 83 residues processed: 243 average time/residue: 1.0076 time to fit residues: 398.1375 Evaluate side-chains 233 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 145 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 705 ARG Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 727 ILE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain C residue 940 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain D residue 941 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 734 SER Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 543 GLU Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 0.9980 chunk 438 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 305 optimal weight: 0.5980 chunk 460 optimal weight: 7.9990 chunk 423 optimal weight: 4.9990 chunk 366 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS C 219 GLN E 509 GLN F 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37608 Z= 0.186 Angle : 0.584 8.543 50802 Z= 0.297 Chirality : 0.040 0.377 5832 Planarity : 0.004 0.053 6522 Dihedral : 7.389 167.205 5120 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.63 % Allowed : 19.33 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4632 helix: 0.91 (0.11), residues: 2164 sheet: -2.04 (0.22), residues: 534 loop : -1.76 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 464 HIS 0.009 0.001 HIS A 491 PHE 0.022 0.002 PHE B 619 TYR 0.019 0.001 TYR F 939 ARG 0.013 0.001 ARG C 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 148 time to evaluate : 5.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 937 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: D 651 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8272 (p0) outliers start: 66 outliers final: 58 residues processed: 209 average time/residue: 0.9800 time to fit residues: 339.8996 Evaluate side-chains 206 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 146 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 858 CYS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain C residue 940 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 ASP Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 909 CYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 940 ARG Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 751 PHE Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain E residue 940 ARG Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 543 GLU Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 3.9990 chunk 390 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 337 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 367 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 376 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS C 460 ASN E 509 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.127483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.093868 restraints weight = 442006.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.094795 restraints weight = 195147.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.094932 restraints weight = 104699.768| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37608 Z= 0.178 Angle : 0.558 8.964 50802 Z= 0.282 Chirality : 0.040 0.389 5832 Planarity : 0.004 0.050 6522 Dihedral : 7.149 164.414 5120 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.56 % Allowed : 19.46 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 4632 helix: 1.24 (0.11), residues: 2164 sheet: -2.06 (0.21), residues: 556 loop : -1.58 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 464 HIS 0.009 0.001 HIS B 187 PHE 0.019 0.001 PHE B 619 TYR 0.015 0.001 TYR F 939 ARG 0.009 0.000 ARG B 511 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9456.08 seconds wall clock time: 164 minutes 20.59 seconds (9860.59 seconds total)