Starting phenix.real_space_refine on Tue Feb 20 12:49:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz6_24752/02_2024/7rz6_24752_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz6_24752/02_2024/7rz6_24752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz6_24752/02_2024/7rz6_24752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz6_24752/02_2024/7rz6_24752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz6_24752/02_2024/7rz6_24752_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz6_24752/02_2024/7rz6_24752_updated.pdb" } resolution = 4.4 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= 0.002 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 142 5.16 5 C 17972 2.51 5 N 4596 2.21 5 O 5210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "B GLU 1301": "OE1" <-> "OE2" Residue "D GLU 1301": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27922 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7740 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 956} Chain breaks: 4 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "C" Number of atoms: 7740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7740 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 956} Chain breaks: 4 Chain: "D" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 15.60, per 1000 atoms: 0.56 Number of scatterers: 27922 At special positions: 0 Unit cell: (125.892, 164.628, 190.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 2 15.00 O 5210 8.00 N 4596 7.00 C 17972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.92 Conformation dependent library (CDL) restraints added in 5.3 seconds 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 22 sheets defined 44.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.580A pdb=" N GLY A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.531A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.525A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.571A pdb=" N THR A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.179A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.617A pdb=" N THR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.633A pdb=" N ALA A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.516A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 520 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.943A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 629 removed outlier: 3.555A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 658 No H-bonds generated for 'chain 'A' and resid 655 through 658' Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.798A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.643A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.616A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 4.327A pdb=" N VAL A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 753 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.597A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 818 removed outlier: 3.736A pdb=" N ALA A 793 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLY A 794 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 795 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 800 " --> pdb=" O TYR A 797 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 801 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 804 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 805 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 807 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 815 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 817 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 4.046A pdb=" N ALA A 836 " --> pdb=" O CYS A 832 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 854 " --> pdb=" O GLY A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 950 removed outlier: 3.777A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 929 " --> pdb=" O ILE A 925 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.825A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 4.076A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 3.797A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1034 " --> pdb=" O LYS A1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.903A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.711A pdb=" N VAL B 82 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 86 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 89 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.735A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.531A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.604A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.768A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.602A pdb=" N GLU B 330 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS B 334 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.545A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.579A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.848A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.830A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 641 No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 754 Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.513A pdb=" N LEU B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 779 No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 793 through 820 removed outlier: 3.604A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.579A pdb=" N GLY C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.532A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.524A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.572A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 233 through 237 removed outlier: 4.180A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 237' Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.616A pdb=" N THR C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.632A pdb=" N ALA C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.517A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 520 Proline residue: C 520 - end of helix Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.943A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 629 removed outlier: 3.555A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 655 through 658 No H-bonds generated for 'chain 'C' and resid 655 through 658' Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.798A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.642A pdb=" N ILE C 712 " --> pdb=" O MET C 708 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 755 removed outlier: 3.616A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 4.326A pdb=" N VAL C 750 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.599A pdb=" N LYS C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 818 removed outlier: 3.736A pdb=" N ALA C 793 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLY C 794 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 795 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 800 " --> pdb=" O TYR C 797 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 801 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 804 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 805 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 807 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 813 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS C 815 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS C 817 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 4.047A pdb=" N ALA C 836 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 843 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 854 " --> pdb=" O GLY C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 950 removed outlier: 3.776A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 928 " --> pdb=" O MET C 924 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 929 " --> pdb=" O ILE C 925 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.825A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 937 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 4.077A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 972 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 989 " --> pdb=" O ASN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1034 removed outlier: 3.797A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C1016 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C1017 " --> pdb=" O SER C1013 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C1022 " --> pdb=" O GLU C1018 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1034 " --> pdb=" O LYS C1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.903A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.711A pdb=" N VAL D 82 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN D 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR D 86 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.735A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 156 removed outlier: 3.532A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.604A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 280 through 299 removed outlier: 3.769A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 291 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.602A pdb=" N GLU D 330 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS D 334 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.545A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 523 through 545 removed outlier: 3.578A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.847A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.829A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 641 No H-bonds generated for 'chain 'D' and resid 638 through 641' Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 754 Processing helix chain 'D' and resid 758 through 768 removed outlier: 3.512A pdb=" N LEU D 762 " --> pdb=" O VAL D 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 779 No H-bonds generated for 'chain 'D' and resid 776 through 779' Processing helix chain 'D' and resid 793 through 820 removed outlier: 3.604A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 removed outlier: 7.113A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER A 95 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY A 75 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 97 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.400A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= D, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= E, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.683A pdb=" N MET A 721 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 997 through 1003 removed outlier: 3.585A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A1002 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 862 " --> pdb=" O SER A 884 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 884 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 883 " --> pdb=" O CYS A 890 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 890 " --> pdb=" O HIS A 883 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.516A pdb=" N ARG B 42 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 73 through 75 removed outlier: 6.021A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= J, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.210A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 358 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.640A pdb=" N TYR B 702 " --> pdb=" O MET B 503 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 42 through 50 removed outlier: 7.113A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER C 95 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY C 75 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE C 97 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.402A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= O, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.683A pdb=" N MET C 721 " --> pdb=" O ILE C 504 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 997 through 1003 removed outlier: 3.585A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C1002 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 862 " --> pdb=" O SER C 884 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER C 884 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 883 " --> pdb=" O CYS C 890 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS C 890 " --> pdb=" O HIS C 883 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.515A pdb=" N ARG D 42 " --> pdb=" O ILE D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 73 through 75 removed outlier: 6.021A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= U, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.210A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 358 " --> pdb=" O TRP D 374 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.640A pdb=" N TYR D 702 " --> pdb=" O MET D 503 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2898 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: 9.47 Time building geometry restraints manager: 11.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4570 1.31 - 1.44: 7741 1.44 - 1.57: 15955 1.57 - 1.70: 6 1.70 - 1.83: 232 Bond restraints: 28504 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.431 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.430 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 PCW C1101 " pdb=" C32 PCW C1101 " ideal model delta sigma weight residual 1.502 1.558 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C31 PCW A1101 " pdb=" C32 PCW A1101 " ideal model delta sigma weight residual 1.502 1.557 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" CA THR C 457 " pdb=" C THR C 457 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.34e-02 5.57e+03 6.93e+00 ... (remaining 28499 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.50: 595 106.50 - 113.82: 15938 113.82 - 121.13: 14443 121.13 - 128.45: 7336 128.45 - 135.76: 186 Bond angle restraints: 38498 Sorted by residual: angle pdb=" CA LEU C 43 " pdb=" CB LEU C 43 " pdb=" CG LEU C 43 " ideal model delta sigma weight residual 116.30 135.76 -19.46 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 135.74 -19.44 3.50e+00 8.16e-02 3.08e+01 angle pdb=" N ILE A 304 " pdb=" CA ILE A 304 " pdb=" C ILE A 304 " ideal model delta sigma weight residual 111.91 107.15 4.76 8.90e-01 1.26e+00 2.86e+01 angle pdb=" N ILE C 304 " pdb=" CA ILE C 304 " pdb=" C ILE C 304 " ideal model delta sigma weight residual 111.91 107.16 4.75 8.90e-01 1.26e+00 2.84e+01 angle pdb=" C THR A 457 " pdb=" N LYS A 458 " pdb=" CA LYS A 458 " ideal model delta sigma weight residual 122.07 129.00 -6.93 1.43e+00 4.89e-01 2.35e+01 ... (remaining 38493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 15827 15.11 - 30.22: 765 30.22 - 45.33: 280 45.33 - 60.45: 32 60.45 - 75.56: 12 Dihedral angle restraints: 16916 sinusoidal: 6744 harmonic: 10172 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 168.56 -75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 168.55 -75.55 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CA LYS A 716 " pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta harmonic sigma weight residual 180.00 139.50 40.50 0 5.00e+00 4.00e-02 6.56e+01 ... (remaining 16913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3394 0.057 - 0.115: 737 0.115 - 0.172: 134 0.172 - 0.229: 13 0.229 - 0.286: 4 Chirality restraints: 4282 Sorted by residual: chirality pdb=" CG LEU A 882 " pdb=" CB LEU A 882 " pdb=" CD1 LEU A 882 " pdb=" CD2 LEU A 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU C 882 " pdb=" CB LEU C 882 " pdb=" CD1 LEU C 882 " pdb=" CD2 LEU C 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU A 989 " pdb=" CB LEU A 989 " pdb=" CD1 LEU A 989 " pdb=" CD2 LEU A 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4279 not shown) Planarity restraints: 4848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO C 717 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 717 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 99 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.044 5.00e-02 4.00e+02 ... (remaining 4845 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3658 2.75 - 3.29: 27234 3.29 - 3.83: 45647 3.83 - 4.36: 53537 4.36 - 4.90: 88733 Nonbonded interactions: 218809 Sorted by model distance: nonbonded pdb=" OG SER C 87 " pdb=" OD1 ASN D 54 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.220 2.440 nonbonded pdb=" OG SER C 662 " pdb=" OD1 ASP C 668 " model vdw 2.281 2.440 nonbonded pdb=" OG SER A 662 " pdb=" OD1 ASP A 668 " model vdw 2.282 2.440 ... (remaining 218804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.850 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 76.410 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 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 : 0.005 0.098 28504 Z= 0.312 Angle : 0.928 19.460 38498 Z= 0.497 Chirality : 0.050 0.286 4282 Planarity : 0.007 0.103 4848 Dihedral : 10.731 74.759 10386 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.46 % Allowed : 4.97 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.12 % 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: -4.26 (0.11), residues: 3502 helix: -3.13 (0.08), residues: 1608 sheet: -1.87 (0.23), residues: 432 loop : -2.57 (0.13), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 323 HIS 0.012 0.002 HIS A 214 PHE 0.021 0.002 PHE D 101 TYR 0.019 0.002 TYR C 768 ARG 0.007 0.001 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 858 time to evaluate : 3.305 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 43 LEU cc_start: -0.1197 (OUTLIER) cc_final: -0.1742 (mp) REVERT: A 60 ASN cc_start: 0.6301 (m-40) cc_final: 0.5542 (t0) REVERT: A 113 MET cc_start: 0.3719 (tpp) cc_final: 0.2800 (tpp) REVERT: A 292 MET cc_start: 0.5632 (mtt) cc_final: 0.5024 (mmp) REVERT: A 408 MET cc_start: 0.6947 (mmt) cc_final: 0.6665 (mmp) REVERT: A 574 PHE cc_start: 0.7041 (t80) cc_final: 0.6750 (m-80) REVERT: A 674 MET cc_start: 0.7844 (mtm) cc_final: 0.7514 (ttm) REVERT: A 702 TYR cc_start: 0.5965 (t80) cc_final: 0.5111 (t80) REVERT: A 707 THR cc_start: 0.6838 (m) cc_final: 0.6470 (t) REVERT: A 907 MET cc_start: 0.6706 (mtm) cc_final: 0.6236 (tpt) REVERT: A 924 MET cc_start: 0.8565 (mmp) cc_final: 0.8058 (mmm) REVERT: A 935 SER cc_start: 0.7605 (m) cc_final: 0.7305 (p) REVERT: B 26 TYR cc_start: 0.8012 (t80) cc_final: 0.7748 (t80) REVERT: B 27 SER cc_start: 0.7477 (m) cc_final: 0.6692 (p) REVERT: B 220 TYR cc_start: 0.6126 (m-80) cc_final: 0.5828 (m-80) REVERT: B 271 PRO cc_start: 0.6008 (Cg_endo) cc_final: 0.5789 (Cg_exo) REVERT: B 382 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6006 (pp) REVERT: B 518 LEU cc_start: 0.7506 (pp) cc_final: 0.6172 (pp) REVERT: B 708 MET cc_start: 0.7401 (ttm) cc_final: 0.7046 (tpt) REVERT: B 711 TYR cc_start: 0.8024 (t80) cc_final: 0.7424 (t80) REVERT: B 797 TYR cc_start: 0.7213 (m-80) cc_final: 0.6071 (t80) REVERT: B 805 LEU cc_start: 0.7966 (tt) cc_final: 0.7679 (pp) REVERT: C 12 ILE cc_start: 0.6940 (pp) cc_final: 0.6423 (pt) REVERT: C 93 HIS cc_start: 0.5582 (m90) cc_final: 0.5119 (m-70) REVERT: C 255 VAL cc_start: 0.8538 (t) cc_final: 0.7999 (t) REVERT: C 479 LEU cc_start: 0.8142 (tp) cc_final: 0.7835 (mt) REVERT: C 593 PRO cc_start: 0.6080 (Cg_exo) cc_final: 0.5675 (Cg_endo) REVERT: C 633 ILE cc_start: 0.5887 (pp) cc_final: 0.4935 (pt) REVERT: C 713 GLU cc_start: 0.8423 (tt0) cc_final: 0.8113 (tm-30) REVERT: C 891 PHE cc_start: 0.6498 (m-10) cc_final: 0.5255 (m-10) REVERT: C 907 MET cc_start: 0.3489 (mtm) cc_final: 0.3071 (mmp) REVERT: C 920 ASN cc_start: 0.8408 (t160) cc_final: 0.8015 (t0) REVERT: C 921 VAL cc_start: 0.6633 (t) cc_final: 0.6223 (t) REVERT: C 960 PHE cc_start: 0.7668 (t80) cc_final: 0.7354 (t80) REVERT: C 983 SER cc_start: 0.8017 (m) cc_final: 0.7690 (p) REVERT: C 1001 TYR cc_start: 0.8557 (p90) cc_final: 0.7746 (p90) REVERT: D 97 ILE cc_start: 0.8110 (mp) cc_final: 0.7734 (mp) REVERT: D 124 LEU cc_start: 0.7637 (tp) cc_final: 0.7381 (tp) REVERT: D 204 ILE cc_start: 0.5950 (mt) cc_final: 0.5375 (pt) REVERT: D 684 ARG cc_start: 0.6597 (pmt170) cc_final: 0.5592 (tpm170) REVERT: D 720 THR cc_start: 0.7409 (p) cc_final: 0.5886 (p) REVERT: D 721 MET cc_start: 0.8868 (ttt) cc_final: 0.7942 (ttp) outliers start: 14 outliers final: 4 residues processed: 870 average time/residue: 0.4587 time to fit residues: 597.1587 Evaluate side-chains 473 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 467 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.8980 chunk 266 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 214 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 359 ASN B 411 ASN B 461 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 246 GLN C 412 HIS ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 950 HIS C 985 ASN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 355 ASN D 411 ASN D 412 HIS D 435 HIS ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 28504 Z= 0.436 Angle : 0.939 14.103 38498 Z= 0.498 Chirality : 0.050 0.253 4282 Planarity : 0.007 0.104 4848 Dihedral : 6.996 59.387 3860 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.43 % Allowed : 5.63 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -2.74 (0.12), residues: 3502 helix: -1.36 (0.11), residues: 1654 sheet: -1.63 (0.28), residues: 308 loop : -2.30 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 526 HIS 0.012 0.003 HIS A 219 PHE 0.060 0.004 PHE B 658 TYR 0.036 0.003 TYR D 135 ARG 0.015 0.001 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 661 time to evaluate : 3.299 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: A 333 LEU cc_start: 0.7406 (mt) cc_final: 0.7166 (mt) REVERT: A 358 ILE cc_start: 0.6822 (mt) cc_final: 0.6477 (mt) REVERT: A 408 MET cc_start: 0.7017 (mmt) cc_final: 0.6621 (mmp) REVERT: A 496 MET cc_start: 0.7248 (tpp) cc_final: 0.6929 (ppp) REVERT: A 527 MET cc_start: 0.6809 (tpt) cc_final: 0.5063 (mmt) REVERT: A 531 PHE cc_start: 0.7408 (m-10) cc_final: 0.6664 (m-80) REVERT: A 584 PHE cc_start: 0.8751 (t80) cc_final: 0.8192 (t80) REVERT: A 585 MET cc_start: 0.8352 (tpp) cc_final: 0.8120 (tpp) REVERT: A 605 TRP cc_start: 0.8475 (t-100) cc_final: 0.6913 (t-100) REVERT: A 608 PHE cc_start: 0.8128 (t80) cc_final: 0.7903 (t80) REVERT: A 619 ASN cc_start: 0.7383 (t0) cc_final: 0.6487 (t0) REVERT: A 702 TYR cc_start: 0.7378 (t80) cc_final: 0.7131 (t80) REVERT: A 707 THR cc_start: 0.7989 (m) cc_final: 0.7245 (t) REVERT: A 721 MET cc_start: 0.6542 (ppp) cc_final: 0.6147 (ppp) REVERT: A 988 MET cc_start: 0.6699 (ttm) cc_final: 0.5874 (mtp) REVERT: A 1002 LYS cc_start: 0.4808 (ttpp) cc_final: 0.4533 (mttt) REVERT: A 1005 TRP cc_start: 0.3942 (m100) cc_final: 0.2733 (m-10) REVERT: B 25 GLU cc_start: 0.7594 (mp0) cc_final: 0.6377 (mp0) REVERT: B 316 LEU cc_start: 0.4930 (mt) cc_final: 0.4148 (pp) REVERT: B 329 ILE cc_start: 0.6904 (mt) cc_final: 0.6238 (mt) REVERT: B 503 MET cc_start: 0.4532 (ttm) cc_final: 0.4280 (tmm) REVERT: B 518 LEU cc_start: 0.7311 (pp) cc_final: 0.6991 (pp) REVERT: B 527 MET cc_start: 0.8511 (mmm) cc_final: 0.7330 (mmt) REVERT: B 531 PHE cc_start: 0.8643 (m-80) cc_final: 0.8298 (m-80) REVERT: B 536 VAL cc_start: 0.8996 (t) cc_final: 0.8738 (t) REVERT: B 591 ILE cc_start: 0.8912 (tp) cc_final: 0.8694 (pt) REVERT: B 606 TRP cc_start: 0.8530 (m-10) cc_final: 0.8247 (m-10) REVERT: B 661 ARG cc_start: 0.8078 (pmt-80) cc_final: 0.6909 (ptm160) REVERT: B 732 TYR cc_start: 0.7149 (m-10) cc_final: 0.6319 (m-10) REVERT: B 797 TYR cc_start: 0.7600 (m-80) cc_final: 0.6958 (t80) REVERT: C 55 SER cc_start: 0.9219 (m) cc_final: 0.9002 (t) REVERT: C 109 PHE cc_start: 0.7824 (m-80) cc_final: 0.7053 (m-10) REVERT: C 112 GLN cc_start: 0.7669 (mp10) cc_final: 0.7297 (pm20) REVERT: C 125 ILE cc_start: 0.7290 (mm) cc_final: 0.6496 (mm) REVERT: C 138 ASP cc_start: 0.7003 (t0) cc_final: 0.6750 (p0) REVERT: C 407 MET cc_start: 0.7872 (mmm) cc_final: 0.7405 (mmm) REVERT: C 453 ARG cc_start: 0.5279 (ptp90) cc_final: 0.4221 (ttm110) REVERT: C 503 MET cc_start: 0.8153 (ppp) cc_final: 0.7938 (ppp) REVERT: C 524 GLU cc_start: 0.5630 (pp20) cc_final: 0.5249 (pp20) REVERT: C 629 MET cc_start: 0.8449 (ptt) cc_final: 0.7566 (ppp) REVERT: C 722 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8501 (tttt) REVERT: C 907 MET cc_start: 0.4190 (mtm) cc_final: 0.3528 (mmt) REVERT: C 924 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7422 (mmp) REVERT: C 1023 MET cc_start: 0.7774 (mtm) cc_final: 0.7379 (mtt) REVERT: C 1029 MET cc_start: 0.7373 (tmm) cc_final: 0.6630 (ttm) REVERT: D 54 ASN cc_start: 0.7667 (t0) cc_final: 0.6826 (t0) REVERT: D 81 SER cc_start: 0.8826 (p) cc_final: 0.8337 (m) REVERT: D 189 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7236 (mm-30) REVERT: D 207 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: D 408 MET cc_start: 0.7064 (tpp) cc_final: 0.6701 (tpp) REVERT: D 503 MET cc_start: 0.7701 (tpp) cc_final: 0.7321 (tpt) REVERT: D 619 ASN cc_start: 0.8694 (t0) cc_final: 0.8021 (t0) REVERT: D 686 THR cc_start: 0.6696 (m) cc_final: 0.4958 (m) REVERT: D 721 MET cc_start: 0.8530 (ttt) cc_final: 0.8262 (ttm) outliers start: 13 outliers final: 3 residues processed: 672 average time/residue: 0.4263 time to fit residues: 463.4065 Evaluate side-chains 464 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 459 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 320 optimal weight: 0.4980 chunk 345 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 317 optimal weight: 0.0470 chunk 109 optimal weight: 0.9980 chunk 256 optimal weight: 9.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 202 ASN C 214 HIS C 246 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN C 872 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 236 GLN D 355 ASN D 359 ASN D 575 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.7830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28504 Z= 0.159 Angle : 0.573 8.537 38498 Z= 0.298 Chirality : 0.042 0.198 4282 Planarity : 0.004 0.083 4848 Dihedral : 5.848 53.063 3860 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -1.58 (0.13), residues: 3502 helix: -0.17 (0.12), residues: 1656 sheet: -1.12 (0.26), residues: 390 loop : -2.02 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 460 HIS 0.005 0.001 HIS A 46 PHE 0.027 0.002 PHE C 62 TYR 0.024 0.001 TYR C 980 ARG 0.005 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 3.238 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: A 49 ASN cc_start: 0.4745 (t0) cc_final: 0.4082 (t0) REVERT: A 78 ASP cc_start: 0.5562 (t0) cc_final: 0.5008 (p0) REVERT: A 292 MET cc_start: 0.5491 (mtt) cc_final: 0.4783 (mmp) REVERT: A 359 ASN cc_start: 0.5972 (m-40) cc_final: 0.5741 (m-40) REVERT: A 408 MET cc_start: 0.6957 (mmt) cc_final: 0.6580 (mmp) REVERT: A 523 TYR cc_start: 0.7078 (m-10) cc_final: 0.6495 (m-10) REVERT: A 524 GLU cc_start: 0.7312 (mp0) cc_final: 0.6771 (pp20) REVERT: A 525 ILE cc_start: 0.7978 (mt) cc_final: 0.7404 (mt) REVERT: A 527 MET cc_start: 0.6338 (tpt) cc_final: 0.5327 (tpt) REVERT: A 528 CYS cc_start: 0.7864 (m) cc_final: 0.7183 (m) REVERT: A 531 PHE cc_start: 0.7489 (m-10) cc_final: 0.7268 (m-80) REVERT: A 584 PHE cc_start: 0.8438 (t80) cc_final: 0.8184 (t80) REVERT: A 608 PHE cc_start: 0.8235 (t80) cc_final: 0.7739 (t80) REVERT: A 619 ASN cc_start: 0.8017 (t0) cc_final: 0.7232 (t0) REVERT: A 702 TYR cc_start: 0.7252 (t80) cc_final: 0.6795 (t80) REVERT: A 707 THR cc_start: 0.8061 (m) cc_final: 0.6928 (t) REVERT: A 721 MET cc_start: 0.6544 (ppp) cc_final: 0.6180 (ppp) REVERT: A 979 LEU cc_start: 0.8687 (mm) cc_final: 0.8480 (mm) REVERT: A 988 MET cc_start: 0.5854 (ttm) cc_final: 0.5509 (ttm) REVERT: A 1005 TRP cc_start: 0.3713 (m100) cc_final: 0.2628 (m-10) REVERT: A 1015 LEU cc_start: 0.8628 (mm) cc_final: 0.8256 (pp) REVERT: B 25 GLU cc_start: 0.7253 (mp0) cc_final: 0.6392 (mp0) REVERT: B 167 ASN cc_start: 0.7533 (p0) cc_final: 0.7269 (p0) REVERT: B 179 SER cc_start: 0.8747 (m) cc_final: 0.8486 (t) REVERT: B 316 LEU cc_start: 0.4524 (mt) cc_final: 0.3948 (pp) REVERT: B 496 MET cc_start: 0.8153 (pmm) cc_final: 0.7845 (pmm) REVERT: B 531 PHE cc_start: 0.8752 (m-80) cc_final: 0.8336 (m-80) REVERT: B 542 LEU cc_start: 0.9171 (mm) cc_final: 0.8947 (mm) REVERT: B 587 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7175 (tp40) REVERT: B 591 ILE cc_start: 0.8919 (tp) cc_final: 0.8699 (pt) REVERT: B 601 VAL cc_start: 0.8993 (t) cc_final: 0.8679 (p) REVERT: B 606 TRP cc_start: 0.8549 (m-10) cc_final: 0.8310 (m-10) REVERT: B 707 THR cc_start: 0.8108 (t) cc_final: 0.7566 (t) REVERT: B 708 MET cc_start: 0.7802 (ttp) cc_final: 0.7509 (ttp) REVERT: B 797 TYR cc_start: 0.7771 (m-80) cc_final: 0.7159 (t80) REVERT: B 807 MET cc_start: 0.8835 (mmm) cc_final: 0.8587 (tmm) REVERT: C 55 SER cc_start: 0.9149 (m) cc_final: 0.8925 (t) REVERT: C 109 PHE cc_start: 0.7766 (m-80) cc_final: 0.6890 (m-10) REVERT: C 112 GLN cc_start: 0.7672 (mp10) cc_final: 0.7299 (pm20) REVERT: C 138 ASP cc_start: 0.7510 (t0) cc_final: 0.7189 (t0) REVERT: C 407 MET cc_start: 0.8035 (mmm) cc_final: 0.7565 (mmm) REVERT: C 474 ILE cc_start: 0.8408 (pt) cc_final: 0.8110 (mp) REVERT: C 629 MET cc_start: 0.8374 (ptt) cc_final: 0.7573 (ppp) REVERT: C 640 SER cc_start: 0.9059 (t) cc_final: 0.8169 (p) REVERT: C 702 TYR cc_start: 0.5718 (t80) cc_final: 0.5152 (t80) REVERT: C 710 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 713 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8463 (tm-30) REVERT: C 722 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8384 (tttt) REVERT: C 907 MET cc_start: 0.3940 (mtm) cc_final: 0.3384 (mmt) REVERT: C 924 MET cc_start: 0.7882 (mtt) cc_final: 0.7605 (mmp) REVERT: C 986 ASP cc_start: 0.8068 (t70) cc_final: 0.7413 (m-30) REVERT: C 1029 MET cc_start: 0.7422 (tmm) cc_final: 0.6769 (ttm) REVERT: D 81 SER cc_start: 0.8574 (p) cc_final: 0.8117 (m) REVERT: D 113 MET cc_start: 0.7006 (mmm) cc_final: 0.6760 (mmm) REVERT: D 174 ASP cc_start: 0.8003 (m-30) cc_final: 0.7105 (m-30) REVERT: D 207 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7842 (mm110) REVERT: D 213 LYS cc_start: 0.8584 (mptt) cc_final: 0.8052 (mmtt) REVERT: D 408 MET cc_start: 0.7019 (tpp) cc_final: 0.6665 (tpp) REVERT: D 503 MET cc_start: 0.8112 (tpp) cc_final: 0.7834 (tpp) REVERT: D 585 MET cc_start: 0.7868 (tpp) cc_final: 0.7496 (tpp) REVERT: D 619 ASN cc_start: 0.8431 (t0) cc_final: 0.7853 (t0) REVERT: D 675 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8067 (tpp-160) REVERT: D 721 MET cc_start: 0.8790 (ttt) cc_final: 0.8519 (ttm) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.3706 time to fit residues: 381.9244 Evaluate side-chains 456 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 321 optimal weight: 0.0020 chunk 340 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 304 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN C 10 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN C 985 ASN D 10 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 1.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 28504 Z= 0.398 Angle : 0.903 11.959 38498 Z= 0.474 Chirality : 0.051 0.307 4282 Planarity : 0.007 0.098 4848 Dihedral : 7.324 84.440 3860 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.27 % Allowed : 5.37 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.06 % 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: -2.09 (0.13), residues: 3502 helix: -0.70 (0.12), residues: 1598 sheet: -1.63 (0.29), residues: 296 loop : -2.01 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 374 HIS 0.015 0.002 HIS B 214 PHE 0.041 0.003 PHE B 245 TYR 0.042 0.003 TYR A 711 ARG 0.016 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 574 time to evaluate : 3.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9347 (tp) cc_final: 0.9106 (tp) REVERT: A 309 ARG cc_start: 0.5334 (mmp-170) cc_final: 0.5127 (ttp80) REVERT: A 406 VAL cc_start: 0.8913 (t) cc_final: 0.8462 (t) REVERT: A 408 MET cc_start: 0.7079 (mmt) cc_final: 0.6683 (mmp) REVERT: A 527 MET cc_start: 0.7530 (tpp) cc_final: 0.7261 (tpp) REVERT: A 571 PHE cc_start: 0.6642 (m-80) cc_final: 0.6375 (m-80) REVERT: A 580 SER cc_start: 0.9668 (m) cc_final: 0.9299 (p) REVERT: A 586 GLN cc_start: 0.8353 (tp40) cc_final: 0.7895 (tp40) REVERT: A 597 SER cc_start: 0.8461 (m) cc_final: 0.7961 (p) REVERT: A 605 TRP cc_start: 0.9069 (t-100) cc_final: 0.8770 (t-100) REVERT: A 619 ASN cc_start: 0.9102 (t0) cc_final: 0.8599 (t0) REVERT: A 629 MET cc_start: 0.7034 (mmp) cc_final: 0.6686 (tpp) REVERT: A 722 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7306 (mtpt) REVERT: A 756 GLN cc_start: 0.7675 (tt0) cc_final: 0.7348 (mp10) REVERT: A 979 LEU cc_start: 0.9297 (mm) cc_final: 0.9089 (mm) REVERT: A 980 TYR cc_start: 0.7297 (t80) cc_final: 0.6606 (t80) REVERT: A 1015 LEU cc_start: 0.8949 (mm) cc_final: 0.8727 (pp) REVERT: A 1026 TYR cc_start: 0.5833 (m-10) cc_final: 0.5444 (m-10) REVERT: B 78 ASP cc_start: 0.7914 (t0) cc_final: 0.7532 (p0) REVERT: B 89 CYS cc_start: 0.8147 (m) cc_final: 0.7773 (p) REVERT: B 97 ILE cc_start: 0.7348 (mp) cc_final: 0.6837 (mp) REVERT: B 316 LEU cc_start: 0.6443 (mt) cc_final: 0.5804 (pp) REVERT: B 363 LEU cc_start: 0.7775 (tp) cc_final: 0.7567 (tt) REVERT: B 670 MET cc_start: 0.8430 (mpp) cc_final: 0.8094 (mtt) REVERT: B 684 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.6937 (mmt-90) REVERT: B 708 MET cc_start: 0.6900 (ttp) cc_final: 0.6302 (ttt) REVERT: B 792 VAL cc_start: 0.9357 (t) cc_final: 0.9089 (p) REVERT: B 797 TYR cc_start: 0.8659 (m-80) cc_final: 0.8197 (t80) REVERT: B 803 LEU cc_start: 0.9332 (mt) cc_final: 0.9126 (mt) REVERT: C 33 MET cc_start: 0.6765 (ptp) cc_final: 0.6088 (ptt) REVERT: C 55 SER cc_start: 0.9294 (m) cc_final: 0.9058 (t) REVERT: C 95 SER cc_start: 0.8161 (m) cc_final: 0.7959 (t) REVERT: C 330 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8066 (tp30) REVERT: C 374 TRP cc_start: 0.7612 (t60) cc_final: 0.7166 (t60) REVERT: C 407 MET cc_start: 0.8183 (mmm) cc_final: 0.7870 (mmm) REVERT: C 511 LYS cc_start: 0.7943 (mmpt) cc_final: 0.7513 (tptt) REVERT: C 524 GLU cc_start: 0.7053 (pp20) cc_final: 0.6279 (pp20) REVERT: C 528 CYS cc_start: 0.8752 (m) cc_final: 0.8485 (m) REVERT: C 587 GLN cc_start: 0.7529 (pp30) cc_final: 0.7205 (pp30) REVERT: C 619 ASN cc_start: 0.9045 (t0) cc_final: 0.8775 (t0) REVERT: C 629 MET cc_start: 0.8550 (ptt) cc_final: 0.7568 (tmm) REVERT: C 649 THR cc_start: 0.8453 (p) cc_final: 0.8229 (p) REVERT: C 713 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8594 (tm-30) REVERT: C 763 LYS cc_start: 0.8813 (tttp) cc_final: 0.8428 (tptt) REVERT: C 920 ASN cc_start: 0.8419 (t0) cc_final: 0.8083 (t0) REVERT: C 921 VAL cc_start: 0.7142 (t) cc_final: 0.6933 (t) REVERT: C 924 MET cc_start: 0.8075 (mtt) cc_final: 0.7540 (mmp) REVERT: C 1005 TRP cc_start: 0.6071 (OUTLIER) cc_final: 0.5671 (m-10) REVERT: C 1029 MET cc_start: 0.8088 (tmm) cc_final: 0.7751 (ttm) REVERT: D 118 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8305 (mttp) REVERT: D 140 ASP cc_start: 0.7513 (m-30) cc_final: 0.7279 (t0) REVERT: D 293 THR cc_start: 0.8835 (m) cc_final: 0.8577 (p) REVERT: D 408 MET cc_start: 0.7246 (tpp) cc_final: 0.7015 (tpp) REVERT: D 503 MET cc_start: 0.8516 (tpp) cc_final: 0.8089 (tpt) REVERT: D 541 PHE cc_start: 0.8662 (t80) cc_final: 0.8304 (t80) REVERT: D 576 SER cc_start: 0.8302 (m) cc_final: 0.7823 (t) REVERT: D 585 MET cc_start: 0.9354 (tpp) cc_final: 0.8421 (mmt) REVERT: D 619 ASN cc_start: 0.9061 (t0) cc_final: 0.8791 (t0) REVERT: D 721 MET cc_start: 0.9144 (ttt) cc_final: 0.8922 (ttm) outliers start: 8 outliers final: 1 residues processed: 578 average time/residue: 0.3946 time to fit residues: 371.9609 Evaluate side-chains 401 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.3980 chunk 193 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN C 202 ASN C 355 ASN C 575 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 1.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28504 Z= 0.201 Angle : 0.618 10.250 38498 Z= 0.320 Chirality : 0.042 0.233 4282 Planarity : 0.004 0.085 4848 Dihedral : 5.972 53.822 3860 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -1.29 (0.14), residues: 3502 helix: 0.12 (0.12), residues: 1610 sheet: -1.38 (0.29), residues: 302 loop : -1.76 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 158 HIS 0.004 0.001 HIS B 214 PHE 0.025 0.002 PHE D 531 TYR 0.026 0.001 TYR A 177 ARG 0.005 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 552 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8259 (t0) cc_final: 0.7208 (p0) REVERT: A 138 ASP cc_start: 0.6424 (t0) cc_final: 0.5084 (t0) REVERT: A 140 ASP cc_start: 0.7770 (m-30) cc_final: 0.7254 (m-30) REVERT: A 248 VAL cc_start: 0.8423 (m) cc_final: 0.7888 (p) REVERT: A 309 ARG cc_start: 0.5279 (mmp-170) cc_final: 0.5004 (ttp80) REVERT: A 408 MET cc_start: 0.6925 (mmt) cc_final: 0.6684 (mmp) REVERT: A 503 MET cc_start: 0.6568 (ttp) cc_final: 0.5914 (ttp) REVERT: A 524 GLU cc_start: 0.8060 (mp0) cc_final: 0.7520 (pp20) REVERT: A 525 ILE cc_start: 0.8865 (mt) cc_final: 0.8550 (mt) REVERT: A 527 MET cc_start: 0.6872 (tpp) cc_final: 0.6425 (mmt) REVERT: A 530 VAL cc_start: 0.9176 (m) cc_final: 0.8904 (p) REVERT: A 580 SER cc_start: 0.9534 (m) cc_final: 0.9209 (p) REVERT: A 619 ASN cc_start: 0.9238 (t0) cc_final: 0.8505 (t0) REVERT: A 670 MET cc_start: 0.8558 (mtm) cc_final: 0.8317 (mtm) REVERT: A 721 MET cc_start: 0.7003 (ppp) cc_final: 0.6187 (ptt) REVERT: A 722 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7224 (mttt) REVERT: A 756 GLN cc_start: 0.7704 (tt0) cc_final: 0.7351 (mp10) REVERT: A 924 MET cc_start: 0.8665 (mmp) cc_final: 0.8437 (mmm) REVERT: A 939 MET cc_start: 0.5818 (ptt) cc_final: 0.5538 (ptm) REVERT: A 980 TYR cc_start: 0.7590 (t80) cc_final: 0.7004 (t80) REVERT: A 981 ILE cc_start: 0.8503 (mp) cc_final: 0.7867 (mp) REVERT: A 1015 LEU cc_start: 0.8951 (mm) cc_final: 0.8705 (pp) REVERT: A 1026 TYR cc_start: 0.5866 (m-10) cc_final: 0.5478 (m-10) REVERT: B 25 GLU cc_start: 0.8232 (mp0) cc_final: 0.7928 (mp0) REVERT: B 56 PHE cc_start: 0.7310 (t80) cc_final: 0.6888 (t80) REVERT: B 78 ASP cc_start: 0.7935 (t0) cc_final: 0.7509 (p0) REVERT: B 363 LEU cc_start: 0.7636 (tp) cc_final: 0.7365 (tt) REVERT: B 578 TRP cc_start: 0.9039 (t-100) cc_final: 0.8025 (t60) REVERT: B 661 ARG cc_start: 0.7948 (pmt-80) cc_final: 0.7373 (pmt-80) REVERT: B 789 LEU cc_start: 0.9331 (tp) cc_final: 0.8857 (tp) REVERT: B 792 VAL cc_start: 0.9410 (t) cc_final: 0.9167 (p) REVERT: B 797 TYR cc_start: 0.8646 (m-80) cc_final: 0.8196 (t80) REVERT: B 813 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7783 (tm-30) REVERT: C 77 TYR cc_start: 0.8874 (p90) cc_final: 0.8298 (p90) REVERT: C 95 SER cc_start: 0.8112 (m) cc_final: 0.6225 (t) REVERT: C 355 ASN cc_start: 0.6013 (OUTLIER) cc_final: 0.5455 (t0) REVERT: C 400 ILE cc_start: 0.8540 (tt) cc_final: 0.8242 (mt) REVERT: C 406 VAL cc_start: 0.8069 (t) cc_final: 0.7616 (t) REVERT: C 511 LYS cc_start: 0.8237 (mmpt) cc_final: 0.7784 (tptt) REVERT: C 524 GLU cc_start: 0.7236 (pp20) cc_final: 0.6118 (pp20) REVERT: C 525 ILE cc_start: 0.8924 (mt) cc_final: 0.8583 (mt) REVERT: C 528 CYS cc_start: 0.8849 (m) cc_final: 0.8575 (m) REVERT: C 619 ASN cc_start: 0.8991 (t0) cc_final: 0.8629 (t0) REVERT: C 629 MET cc_start: 0.8650 (ptt) cc_final: 0.8023 (tmm) REVERT: C 713 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8702 (tm-30) REVERT: C 763 LYS cc_start: 0.8788 (tttp) cc_final: 0.8419 (tptt) REVERT: C 924 MET cc_start: 0.7985 (mtt) cc_final: 0.7603 (mmp) REVERT: D 140 ASP cc_start: 0.7641 (m-30) cc_final: 0.7359 (t0) REVERT: D 189 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8294 (tp30) REVERT: D 293 THR cc_start: 0.8719 (m) cc_final: 0.8489 (p) REVERT: D 408 MET cc_start: 0.7162 (tpp) cc_final: 0.6949 (tpp) REVERT: D 496 MET cc_start: 0.5607 (pmm) cc_final: 0.4830 (pmm) REVERT: D 541 PHE cc_start: 0.8644 (t80) cc_final: 0.8257 (t80) REVERT: D 576 SER cc_start: 0.8191 (m) cc_final: 0.7666 (t) REVERT: D 585 MET cc_start: 0.8876 (tpp) cc_final: 0.8455 (tpp) REVERT: D 619 ASN cc_start: 0.9277 (t0) cc_final: 0.8844 (t0) REVERT: D 620 LEU cc_start: 0.9532 (tp) cc_final: 0.9302 (tp) REVERT: D 624 LEU cc_start: 0.9581 (mt) cc_final: 0.9381 (mp) REVERT: D 721 MET cc_start: 0.9230 (ttt) cc_final: 0.8955 (ttm) REVERT: D 789 LEU cc_start: 0.8926 (tp) cc_final: 0.8559 (tp) outliers start: 3 outliers final: 1 residues processed: 554 average time/residue: 0.3652 time to fit residues: 330.4119 Evaluate side-chains 404 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 402 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 10 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 1.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28504 Z= 0.344 Angle : 0.748 11.464 38498 Z= 0.392 Chirality : 0.046 0.376 4282 Planarity : 0.005 0.089 4848 Dihedral : 6.247 61.585 3860 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -1.53 (0.13), residues: 3502 helix: -0.09 (0.12), residues: 1610 sheet: -1.64 (0.29), residues: 310 loop : -1.84 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 323 HIS 0.009 0.002 HIS B 214 PHE 0.027 0.002 PHE C 29 TYR 0.030 0.002 TYR C 980 ARG 0.008 0.001 ARG D 675 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9096 (mp0) cc_final: 0.8842 (mp0) REVERT: A 50 LEU cc_start: 0.8988 (pt) cc_final: 0.8756 (pt) REVERT: A 204 ILE cc_start: 0.9253 (mt) cc_final: 0.9044 (mt) REVERT: A 225 LEU cc_start: 0.7980 (tp) cc_final: 0.7598 (tp) REVERT: A 248 VAL cc_start: 0.8627 (m) cc_final: 0.7925 (p) REVERT: A 361 MET cc_start: 0.6428 (mpp) cc_final: 0.6049 (mpp) REVERT: A 406 VAL cc_start: 0.8618 (t) cc_final: 0.8283 (t) REVERT: A 408 MET cc_start: 0.6826 (mmt) cc_final: 0.6450 (mmm) REVERT: A 511 LYS cc_start: 0.8032 (mmpt) cc_final: 0.7586 (tppt) REVERT: A 524 GLU cc_start: 0.8132 (mp0) cc_final: 0.7586 (mp0) REVERT: A 580 SER cc_start: 0.9619 (m) cc_final: 0.9362 (p) REVERT: A 619 ASN cc_start: 0.9274 (t0) cc_final: 0.8728 (t0) REVERT: A 721 MET cc_start: 0.7279 (ppp) cc_final: 0.6867 (ptt) REVERT: A 722 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7499 (mttt) REVERT: A 756 GLN cc_start: 0.7659 (tt0) cc_final: 0.7394 (mp10) REVERT: A 797 TYR cc_start: 0.8220 (m-10) cc_final: 0.7800 (m-80) REVERT: A 980 TYR cc_start: 0.7954 (t80) cc_final: 0.7520 (t80) REVERT: A 1026 TYR cc_start: 0.6248 (m-10) cc_final: 0.5732 (m-80) REVERT: B 269 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 511 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8255 (tmtt) REVERT: B 533 TYR cc_start: 0.8979 (t80) cc_final: 0.8764 (t80) REVERT: B 661 ARG cc_start: 0.7995 (pmt-80) cc_final: 0.6845 (mpt180) REVERT: B 813 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8021 (tm-30) REVERT: C 25 GLU cc_start: 0.9436 (mp0) cc_final: 0.9158 (mp0) REVERT: C 126 GLU cc_start: 0.9035 (tt0) cc_final: 0.8694 (mt-10) REVERT: C 435 HIS cc_start: 0.7233 (t-90) cc_final: 0.6937 (t-90) REVERT: C 511 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7694 (tptt) REVERT: C 524 GLU cc_start: 0.7592 (pp20) cc_final: 0.7120 (pp20) REVERT: C 528 CYS cc_start: 0.9001 (m) cc_final: 0.8736 (m) REVERT: C 619 ASN cc_start: 0.9167 (t0) cc_final: 0.8642 (t0) REVERT: C 629 MET cc_start: 0.8622 (ptt) cc_final: 0.8413 (tmm) REVERT: C 783 LYS cc_start: 0.6862 (pptt) cc_final: 0.6194 (mmmt) REVERT: C 924 MET cc_start: 0.7940 (mtt) cc_final: 0.7697 (mmp) REVERT: D 140 ASP cc_start: 0.7868 (m-30) cc_final: 0.7462 (t0) REVERT: D 496 MET cc_start: 0.5725 (pmm) cc_final: 0.5314 (pmm) REVERT: D 503 MET cc_start: 0.8681 (tpp) cc_final: 0.8297 (tpp) REVERT: D 533 TYR cc_start: 0.9159 (t80) cc_final: 0.8947 (t80) REVERT: D 576 SER cc_start: 0.8505 (m) cc_final: 0.8107 (t) REVERT: D 584 PHE cc_start: 0.9456 (t80) cc_final: 0.9207 (t80) REVERT: D 585 MET cc_start: 0.9196 (tpp) cc_final: 0.8728 (tpp) REVERT: D 619 ASN cc_start: 0.9198 (t0) cc_final: 0.8622 (t0) REVERT: D 708 MET cc_start: 0.8649 (tmm) cc_final: 0.7707 (tmm) REVERT: D 721 MET cc_start: 0.9167 (ttt) cc_final: 0.8827 (ttm) outliers start: 1 outliers final: 0 residues processed: 505 average time/residue: 0.3565 time to fit residues: 294.6092 Evaluate side-chains 372 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 248 optimal weight: 0.4980 chunk 192 optimal weight: 4.9990 chunk 286 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 339 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 207 GLN A 302 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 1.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28504 Z= 0.181 Angle : 0.625 16.222 38498 Z= 0.319 Chirality : 0.043 0.436 4282 Planarity : 0.004 0.089 4848 Dihedral : 5.653 60.930 3860 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.10 % Allowed : 1.62 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -1.05 (0.14), residues: 3502 helix: 0.32 (0.13), residues: 1622 sheet: -1.49 (0.26), residues: 380 loop : -1.56 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 605 HIS 0.008 0.001 HIS D 412 PHE 0.040 0.002 PHE B 531 TYR 0.021 0.001 TYR C 980 ARG 0.004 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 520 time to evaluate : 3.299 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: A 25 GLU cc_start: 0.8881 (mp0) cc_final: 0.8623 (mp0) REVERT: A 77 TYR cc_start: 0.8852 (p90) cc_final: 0.8251 (p90) REVERT: A 159 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7795 (mp-120) REVERT: A 177 TYR cc_start: 0.7650 (m-10) cc_final: 0.7438 (m-80) REVERT: A 248 VAL cc_start: 0.8705 (m) cc_final: 0.8184 (p) REVERT: A 408 MET cc_start: 0.6229 (mmt) cc_final: 0.5859 (mmm) REVERT: A 511 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7976 (tppt) REVERT: A 524 GLU cc_start: 0.8032 (mp0) cc_final: 0.7683 (mp0) REVERT: A 540 LEU cc_start: 0.9230 (mm) cc_final: 0.9009 (mm) REVERT: A 580 SER cc_start: 0.9590 (m) cc_final: 0.9356 (p) REVERT: A 585 MET cc_start: 0.8509 (ttm) cc_final: 0.8116 (ttm) REVERT: A 597 SER cc_start: 0.9021 (m) cc_final: 0.8549 (p) REVERT: A 619 ASN cc_start: 0.9292 (t0) cc_final: 0.8637 (t0) REVERT: A 638 ASP cc_start: 0.9112 (m-30) cc_final: 0.8615 (p0) REVERT: A 721 MET cc_start: 0.7243 (ppp) cc_final: 0.6992 (ptt) REVERT: A 722 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7643 (mttt) REVERT: A 797 TYR cc_start: 0.8354 (m-10) cc_final: 0.7920 (m-80) REVERT: A 891 PHE cc_start: 0.5271 (m-10) cc_final: 0.4862 (m-80) REVERT: A 924 MET cc_start: 0.8584 (mmp) cc_final: 0.8321 (mmm) REVERT: A 977 LEU cc_start: 0.9012 (mt) cc_final: 0.8765 (mt) REVERT: A 980 TYR cc_start: 0.7999 (t80) cc_final: 0.7608 (t80) REVERT: A 1026 TYR cc_start: 0.6216 (m-10) cc_final: 0.5683 (m-80) REVERT: B 25 GLU cc_start: 0.8639 (mp0) cc_final: 0.7507 (mp0) REVERT: B 269 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 460 TRP cc_start: 0.2312 (m100) cc_final: 0.2005 (m100) REVERT: B 511 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8121 (tmtt) REVERT: B 661 ARG cc_start: 0.7897 (pmt-80) cc_final: 0.6807 (mpt180) REVERT: B 813 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8083 (tm-30) REVERT: C 62 PHE cc_start: 0.8475 (t80) cc_final: 0.7985 (t80) REVERT: C 126 GLU cc_start: 0.9019 (tt0) cc_final: 0.8755 (mt-10) REVERT: C 361 MET cc_start: 0.8097 (mtp) cc_final: 0.7859 (mtm) REVERT: C 407 MET cc_start: 0.7435 (mmp) cc_final: 0.7120 (mmm) REVERT: C 435 HIS cc_start: 0.7229 (t-90) cc_final: 0.6973 (t-90) REVERT: C 511 LYS cc_start: 0.8328 (mmpt) cc_final: 0.7824 (tptt) REVERT: C 524 GLU cc_start: 0.7670 (pp20) cc_final: 0.7037 (pp20) REVERT: C 528 CYS cc_start: 0.9096 (m) cc_final: 0.8824 (m) REVERT: C 596 LEU cc_start: 0.8333 (tt) cc_final: 0.7875 (tt) REVERT: C 610 LEU cc_start: 0.9092 (mt) cc_final: 0.8828 (mt) REVERT: C 619 ASN cc_start: 0.9031 (t0) cc_final: 0.8534 (t0) REVERT: C 783 LYS cc_start: 0.6934 (pptt) cc_final: 0.6511 (mmmt) REVERT: C 924 MET cc_start: 0.7899 (mtt) cc_final: 0.7684 (mmp) REVERT: D 116 ASP cc_start: 0.9195 (t0) cc_final: 0.8923 (t0) REVERT: D 140 ASP cc_start: 0.7776 (m-30) cc_final: 0.7379 (t0) REVERT: D 361 MET cc_start: 0.8531 (mpp) cc_final: 0.8143 (mpp) REVERT: D 496 MET cc_start: 0.5759 (pmm) cc_final: 0.5180 (pmm) REVERT: D 503 MET cc_start: 0.8718 (tpp) cc_final: 0.8253 (tpp) REVERT: D 576 SER cc_start: 0.8468 (m) cc_final: 0.8060 (t) REVERT: D 585 MET cc_start: 0.9066 (tpp) cc_final: 0.8609 (tpp) REVERT: D 619 ASN cc_start: 0.9101 (t0) cc_final: 0.8676 (t0) REVERT: D 709 ASN cc_start: 0.8312 (t0) cc_final: 0.7949 (t0) REVERT: D 721 MET cc_start: 0.9181 (ttt) cc_final: 0.8935 (ttm) outliers start: 3 outliers final: 0 residues processed: 522 average time/residue: 0.3596 time to fit residues: 307.4780 Evaluate side-chains 400 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 399 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 202 optimal weight: 0.0970 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 290 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN C 412 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 1.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28504 Z= 0.189 Angle : 0.621 9.818 38498 Z= 0.318 Chirality : 0.042 0.268 4282 Planarity : 0.004 0.084 4848 Dihedral : 5.506 58.124 3860 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.07 % Allowed : 1.36 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -0.92 (0.14), residues: 3502 helix: 0.41 (0.13), residues: 1634 sheet: -1.42 (0.27), residues: 342 loop : -1.52 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 766 HIS 0.007 0.001 HIS D 412 PHE 0.026 0.002 PHE A1014 TYR 0.023 0.001 TYR C 980 ARG 0.015 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 501 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8617 (mt0) cc_final: 0.8272 (mp10) REVERT: A 248 VAL cc_start: 0.8715 (m) cc_final: 0.8226 (p) REVERT: A 406 VAL cc_start: 0.8646 (t) cc_final: 0.8425 (t) REVERT: A 408 MET cc_start: 0.6618 (mmt) cc_final: 0.6291 (mmm) REVERT: A 463 MET cc_start: 0.8409 (ppp) cc_final: 0.8045 (ppp) REVERT: A 471 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8119 (mttp) REVERT: A 511 LYS cc_start: 0.8260 (mmpt) cc_final: 0.8000 (tppt) REVERT: A 524 GLU cc_start: 0.8017 (mp0) cc_final: 0.7689 (pp20) REVERT: A 525 ILE cc_start: 0.9265 (mt) cc_final: 0.8818 (mt) REVERT: A 528 CYS cc_start: 0.8724 (m) cc_final: 0.8062 (m) REVERT: A 540 LEU cc_start: 0.9285 (mm) cc_final: 0.8909 (mm) REVERT: A 580 SER cc_start: 0.9625 (m) cc_final: 0.9390 (p) REVERT: A 601 VAL cc_start: 0.9178 (m) cc_final: 0.8946 (p) REVERT: A 619 ASN cc_start: 0.9273 (t0) cc_final: 0.8546 (t0) REVERT: A 638 ASP cc_start: 0.9174 (m-30) cc_final: 0.8771 (p0) REVERT: A 721 MET cc_start: 0.7249 (ppp) cc_final: 0.6991 (ptt) REVERT: A 722 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7599 (mttt) REVERT: A 797 TYR cc_start: 0.8292 (m-10) cc_final: 0.7901 (m-80) REVERT: A 891 PHE cc_start: 0.5592 (m-10) cc_final: 0.5106 (m-80) REVERT: A 924 MET cc_start: 0.8538 (mmp) cc_final: 0.8295 (mmm) REVERT: A 980 TYR cc_start: 0.8017 (t80) cc_final: 0.7721 (t80) REVERT: A 981 ILE cc_start: 0.8721 (mp) cc_final: 0.8121 (mp) REVERT: A 1026 TYR cc_start: 0.6384 (m-10) cc_final: 0.5811 (m-80) REVERT: B 25 GLU cc_start: 0.8755 (mp0) cc_final: 0.7688 (mp0) REVERT: B 269 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 511 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8137 (tmtt) REVERT: B 527 MET cc_start: 0.8120 (mtt) cc_final: 0.7900 (mmt) REVERT: B 528 CYS cc_start: 0.8803 (t) cc_final: 0.8471 (t) REVERT: B 661 ARG cc_start: 0.7922 (pmt-80) cc_final: 0.6983 (mpt180) REVERT: B 789 LEU cc_start: 0.9159 (tp) cc_final: 0.8723 (tp) REVERT: B 813 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8047 (tm-30) REVERT: C 362 GLU cc_start: 0.7667 (tt0) cc_final: 0.7335 (tm-30) REVERT: C 511 LYS cc_start: 0.8254 (mmpt) cc_final: 0.7824 (tptt) REVERT: C 525 ILE cc_start: 0.8984 (mt) cc_final: 0.8713 (mm) REVERT: C 585 MET cc_start: 0.9299 (mmm) cc_final: 0.8152 (mmm) REVERT: C 596 LEU cc_start: 0.8356 (tt) cc_final: 0.7944 (tt) REVERT: C 610 LEU cc_start: 0.9062 (mt) cc_final: 0.8828 (mt) REVERT: C 619 ASN cc_start: 0.9008 (t0) cc_final: 0.8593 (t0) REVERT: C 649 THR cc_start: 0.8264 (p) cc_final: 0.8052 (p) REVERT: C 813 GLU cc_start: 0.7876 (tt0) cc_final: 0.7473 (mm-30) REVERT: C 985 ASN cc_start: 0.8556 (m-40) cc_final: 0.8324 (m-40) REVERT: D 140 ASP cc_start: 0.7826 (m-30) cc_final: 0.7441 (t0) REVERT: D 229 ASP cc_start: 0.8246 (m-30) cc_final: 0.7866 (m-30) REVERT: D 260 GLU cc_start: 0.9049 (mp0) cc_final: 0.8824 (mp0) REVERT: D 269 GLU cc_start: 0.8245 (pp20) cc_final: 0.8009 (mp0) REVERT: D 463 MET cc_start: 0.5747 (ttt) cc_final: 0.5212 (tmm) REVERT: D 496 MET cc_start: 0.5690 (pmm) cc_final: 0.5250 (pmm) REVERT: D 503 MET cc_start: 0.8774 (tpp) cc_final: 0.8255 (tpp) REVERT: D 576 SER cc_start: 0.8585 (m) cc_final: 0.8099 (t) REVERT: D 585 MET cc_start: 0.9100 (tpp) cc_final: 0.8560 (tpp) REVERT: D 619 ASN cc_start: 0.9130 (t0) cc_final: 0.8789 (t0) REVERT: D 709 ASN cc_start: 0.8312 (t0) cc_final: 0.8006 (t0) REVERT: D 721 MET cc_start: 0.9179 (ttt) cc_final: 0.8934 (ttm) REVERT: D 807 MET cc_start: 0.8216 (tmm) cc_final: 0.7970 (tmm) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.3500 time to fit residues: 291.4854 Evaluate side-chains 390 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 10.0000 chunk 325 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 324 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 137 optimal weight: 0.0050 chunk 248 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 285 optimal weight: 0.5980 chunk 299 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 569 ASN A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 508 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 714 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 1.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28504 Z= 0.161 Angle : 0.623 9.496 38498 Z= 0.314 Chirality : 0.042 0.259 4282 Planarity : 0.004 0.081 4848 Dihedral : 5.348 59.593 3860 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.07 % Allowed : 0.76 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -0.88 (0.14), residues: 3502 helix: 0.43 (0.13), residues: 1642 sheet: -1.30 (0.26), residues: 374 loop : -1.50 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 460 HIS 0.008 0.001 HIS B 214 PHE 0.023 0.001 PHE A 608 TYR 0.024 0.001 TYR C 980 ARG 0.010 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 526 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.8779 (p90) cc_final: 0.8309 (p90) REVERT: A 98 THR cc_start: 0.9082 (t) cc_final: 0.8698 (t) REVERT: A 248 VAL cc_start: 0.8689 (m) cc_final: 0.8168 (p) REVERT: A 406 VAL cc_start: 0.8552 (t) cc_final: 0.8317 (t) REVERT: A 463 MET cc_start: 0.8386 (ppp) cc_final: 0.7842 (ppp) REVERT: A 511 LYS cc_start: 0.8222 (mmpt) cc_final: 0.8006 (tppt) REVERT: A 525 ILE cc_start: 0.9338 (mt) cc_final: 0.8221 (mt) REVERT: A 528 CYS cc_start: 0.8686 (m) cc_final: 0.8294 (m) REVERT: A 580 SER cc_start: 0.9600 (m) cc_final: 0.9342 (p) REVERT: A 597 SER cc_start: 0.8846 (m) cc_final: 0.8383 (p) REVERT: A 619 ASN cc_start: 0.9270 (t0) cc_final: 0.8485 (t0) REVERT: A 721 MET cc_start: 0.7256 (ppp) cc_final: 0.7044 (ptt) REVERT: A 722 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7652 (mttt) REVERT: A 797 TYR cc_start: 0.8251 (m-10) cc_final: 0.7903 (m-80) REVERT: A 891 PHE cc_start: 0.5729 (m-10) cc_final: 0.5247 (m-80) REVERT: A 924 MET cc_start: 0.8350 (mmp) cc_final: 0.8114 (mmm) REVERT: A 980 TYR cc_start: 0.8215 (t80) cc_final: 0.7967 (t80) REVERT: A 1026 TYR cc_start: 0.6344 (m-10) cc_final: 0.5780 (m-80) REVERT: B 25 GLU cc_start: 0.8721 (mp0) cc_final: 0.7680 (mp0) REVERT: B 269 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 361 MET cc_start: 0.7625 (mtm) cc_final: 0.6727 (mpp) REVERT: B 460 TRP cc_start: 0.2124 (m100) cc_final: 0.1870 (m100) REVERT: B 511 LYS cc_start: 0.8514 (tmtt) cc_final: 0.8114 (tmtt) REVERT: B 527 MET cc_start: 0.8208 (mtt) cc_final: 0.7562 (mmt) REVERT: B 528 CYS cc_start: 0.8735 (t) cc_final: 0.8416 (t) REVERT: B 531 PHE cc_start: 0.8825 (m-80) cc_final: 0.8549 (m-80) REVERT: B 661 ARG cc_start: 0.7888 (pmt-80) cc_final: 0.6972 (mpt180) REVERT: B 732 TYR cc_start: 0.7435 (m-10) cc_final: 0.7126 (m-80) REVERT: C 62 PHE cc_start: 0.8512 (t80) cc_final: 0.8128 (t80) REVERT: C 113 MET cc_start: 0.7700 (tpp) cc_final: 0.7480 (tpp) REVERT: C 126 GLU cc_start: 0.9027 (tt0) cc_final: 0.8781 (mt-10) REVERT: C 362 GLU cc_start: 0.7469 (tt0) cc_final: 0.7261 (tm-30) REVERT: C 511 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7854 (tptt) REVERT: C 525 ILE cc_start: 0.9023 (mt) cc_final: 0.8649 (mm) REVERT: C 596 LEU cc_start: 0.8292 (tt) cc_final: 0.7889 (tt) REVERT: C 619 ASN cc_start: 0.9021 (t0) cc_final: 0.8587 (t0) REVERT: C 629 MET cc_start: 0.8164 (ttp) cc_final: 0.7890 (ttp) REVERT: C 649 THR cc_start: 0.7967 (p) cc_final: 0.7755 (p) REVERT: C 813 GLU cc_start: 0.7907 (tt0) cc_final: 0.7491 (mm-30) REVERT: C 880 MET cc_start: 0.3080 (tmm) cc_final: 0.2819 (tmm) REVERT: D 140 ASP cc_start: 0.7753 (m-30) cc_final: 0.7412 (t0) REVERT: D 193 ILE cc_start: 0.9159 (mt) cc_final: 0.8898 (mm) REVERT: D 229 ASP cc_start: 0.8212 (m-30) cc_final: 0.7854 (m-30) REVERT: D 269 GLU cc_start: 0.8218 (pp20) cc_final: 0.8016 (mp0) REVERT: D 361 MET cc_start: 0.8294 (mpp) cc_final: 0.7917 (mpp) REVERT: D 463 MET cc_start: 0.5961 (ttt) cc_final: 0.5509 (tmm) REVERT: D 496 MET cc_start: 0.5623 (pmm) cc_final: 0.5105 (pmm) REVERT: D 503 MET cc_start: 0.8822 (tpp) cc_final: 0.8300 (tpp) REVERT: D 576 SER cc_start: 0.8583 (m) cc_final: 0.8171 (t) REVERT: D 585 MET cc_start: 0.9098 (tpp) cc_final: 0.8577 (tpp) REVERT: D 605 TRP cc_start: 0.9028 (t-100) cc_final: 0.8744 (t-100) REVERT: D 709 ASN cc_start: 0.8159 (t0) cc_final: 0.7869 (t0) REVERT: D 721 MET cc_start: 0.9175 (ttt) cc_final: 0.8805 (ttm) outliers start: 2 outliers final: 0 residues processed: 527 average time/residue: 0.3558 time to fit residues: 311.0096 Evaluate side-chains 408 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 2.9990 chunk 207 optimal weight: 0.0570 chunk 334 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 158 optimal weight: 0.0670 chunk 232 optimal weight: 0.2980 chunk 350 optimal weight: 0.9980 chunk 322 optimal weight: 0.4980 chunk 279 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 215 optimal weight: 0.1980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN D 587 GLN D 619 ASN D 714 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 1.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28504 Z= 0.152 Angle : 0.617 9.797 38498 Z= 0.310 Chirality : 0.042 0.207 4282 Planarity : 0.004 0.079 4848 Dihedral : 5.106 59.055 3860 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -0.77 (0.14), residues: 3502 helix: 0.56 (0.13), residues: 1630 sheet: -1.19 (0.27), residues: 366 loop : -1.51 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 460 HIS 0.015 0.001 HIS B 93 PHE 0.033 0.001 PHE A 62 TYR 0.024 0.001 TYR C 768 ARG 0.011 0.000 ARG A 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 508 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7617 (t80) cc_final: 0.7398 (t80) REVERT: A 77 TYR cc_start: 0.8717 (p90) cc_final: 0.8234 (p90) REVERT: A 78 ASP cc_start: 0.8876 (t0) cc_final: 0.7992 (p0) REVERT: A 98 THR cc_start: 0.9122 (t) cc_final: 0.8717 (t) REVERT: A 147 GLN cc_start: 0.8761 (mt0) cc_final: 0.8530 (mp10) REVERT: A 152 SER cc_start: 0.9201 (m) cc_final: 0.8877 (p) REVERT: A 248 VAL cc_start: 0.8666 (m) cc_final: 0.8194 (p) REVERT: A 406 VAL cc_start: 0.8531 (t) cc_final: 0.8298 (t) REVERT: A 408 MET cc_start: 0.5812 (tpp) cc_final: 0.5584 (mmm) REVERT: A 511 LYS cc_start: 0.8215 (mmpt) cc_final: 0.8002 (tppt) REVERT: A 524 GLU cc_start: 0.7974 (pp20) cc_final: 0.6594 (pp20) REVERT: A 528 CYS cc_start: 0.8580 (m) cc_final: 0.8024 (m) REVERT: A 580 SER cc_start: 0.9586 (m) cc_final: 0.9306 (p) REVERT: A 619 ASN cc_start: 0.9203 (t0) cc_final: 0.8484 (t0) REVERT: A 721 MET cc_start: 0.7156 (ppp) cc_final: 0.6893 (ptt) REVERT: A 722 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7660 (mttt) REVERT: A 797 TYR cc_start: 0.8103 (m-10) cc_final: 0.7859 (m-80) REVERT: A 891 PHE cc_start: 0.5586 (m-10) cc_final: 0.5094 (m-80) REVERT: A 980 TYR cc_start: 0.8252 (t80) cc_final: 0.7980 (t80) REVERT: A 1026 TYR cc_start: 0.6149 (m-10) cc_final: 0.5518 (m-80) REVERT: B 25 GLU cc_start: 0.8704 (mp0) cc_final: 0.8354 (mp0) REVERT: B 269 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 361 MET cc_start: 0.7652 (mtm) cc_final: 0.6609 (mpp) REVERT: B 460 TRP cc_start: 0.1998 (m100) cc_final: 0.1738 (m100) REVERT: B 511 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8210 (tmtt) REVERT: B 527 MET cc_start: 0.8061 (mtt) cc_final: 0.7102 (mmm) REVERT: B 528 CYS cc_start: 0.8776 (t) cc_final: 0.8513 (t) REVERT: B 531 PHE cc_start: 0.8841 (m-80) cc_final: 0.8549 (m-80) REVERT: B 661 ARG cc_start: 0.7882 (pmt-80) cc_final: 0.6978 (mpt180) REVERT: B 732 TYR cc_start: 0.7410 (m-10) cc_final: 0.7124 (m-80) REVERT: C 25 GLU cc_start: 0.9374 (mp0) cc_final: 0.8846 (mp0) REVERT: C 147 GLN cc_start: 0.8387 (mp10) cc_final: 0.7666 (mp10) REVERT: C 328 GLU cc_start: 0.8733 (pt0) cc_final: 0.8303 (pm20) REVERT: C 511 LYS cc_start: 0.8423 (mmpt) cc_final: 0.7997 (tptt) REVERT: C 585 MET cc_start: 0.9173 (mmm) cc_final: 0.8615 (mmt) REVERT: C 619 ASN cc_start: 0.9070 (t0) cc_final: 0.8653 (t0) REVERT: C 627 GLU cc_start: 0.8899 (pp20) cc_final: 0.8693 (pp20) REVERT: C 649 THR cc_start: 0.7941 (p) cc_final: 0.7718 (p) REVERT: C 813 GLU cc_start: 0.7886 (tt0) cc_final: 0.7433 (mm-30) REVERT: C 861 TRP cc_start: 0.6939 (m100) cc_final: 0.6597 (m100) REVERT: C 880 MET cc_start: 0.3099 (tmm) cc_final: 0.2883 (tmm) REVERT: D 116 ASP cc_start: 0.8942 (t0) cc_final: 0.8419 (t0) REVERT: D 193 ILE cc_start: 0.9146 (mt) cc_final: 0.8874 (mm) REVERT: D 229 ASP cc_start: 0.8096 (m-30) cc_final: 0.7723 (m-30) REVERT: D 237 PHE cc_start: 0.8073 (m-80) cc_final: 0.7572 (m-80) REVERT: D 269 GLU cc_start: 0.8170 (pp20) cc_final: 0.7953 (mp0) REVERT: D 496 MET cc_start: 0.5827 (pmm) cc_final: 0.5322 (pmm) REVERT: D 503 MET cc_start: 0.8825 (tpp) cc_final: 0.8083 (tpp) REVERT: D 574 PHE cc_start: 0.7582 (t80) cc_final: 0.7100 (m-80) REVERT: D 576 SER cc_start: 0.8555 (m) cc_final: 0.7967 (t) REVERT: D 585 MET cc_start: 0.9183 (tpp) cc_final: 0.8616 (tpp) REVERT: D 605 TRP cc_start: 0.8886 (t-100) cc_final: 0.8653 (t-100) REVERT: D 675 ARG cc_start: 0.8843 (ptp-170) cc_final: 0.8593 (ptp-170) REVERT: D 709 ASN cc_start: 0.8198 (t0) cc_final: 0.7901 (t0) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.3490 time to fit residues: 294.4774 Evaluate side-chains 399 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 297 optimal weight: 0.0970 chunk 85 optimal weight: 0.2980 chunk 257 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN A 147 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.078268 restraints weight = 100032.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081385 restraints weight = 62575.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082274 restraints weight = 38583.061| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 1.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28504 Z= 0.157 Angle : 0.597 8.991 38498 Z= 0.302 Chirality : 0.042 0.287 4282 Planarity : 0.004 0.088 4848 Dihedral : 4.996 59.663 3860 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -0.74 (0.14), residues: 3502 helix: 0.55 (0.13), residues: 1636 sheet: -0.99 (0.27), residues: 358 loop : -1.51 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 460 HIS 0.006 0.001 HIS B 214 PHE 0.028 0.001 PHE A 62 TYR 0.028 0.001 TYR B 127 ARG 0.010 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6728.04 seconds wall clock time: 122 minutes 43.78 seconds (7363.78 seconds total)