Starting phenix.real_space_refine on Mon Nov 20 00:45:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/11_2023/8ss8_40747_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/11_2023/8ss8_40747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/11_2023/8ss8_40747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/11_2023/8ss8_40747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/11_2023/8ss8_40747_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss8_40747/11_2023/8ss8_40747_updated.pdb" } resolution = 2.81 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= 0.009 sd= 0.188 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 S 140 5.16 5 Na 2 4.78 5 C 18450 2.51 5 N 4608 2.21 5 O 5261 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 926": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 926": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28487 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7682 Classifications: {'peptide': 974} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 946} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "C" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7682 Classifications: {'peptide': 974} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 946} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 203 Unusual residues: {' NA': 2, '6ZP': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 201 Unusual residues: {'6ZP': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 15.46, per 1000 atoms: 0.54 Number of scatterers: 28487 At special positions: 0 Unit cell: (117.475, 158.175, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 140 16.00 P 14 15.00 Na 2 11.00 F 12 9.00 O 5261 8.00 N 4608 7.00 C 18450 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=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 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: 11.62 Conformation dependent library (CDL) restraints added in 5.7 seconds 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 32 sheets defined 42.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 127 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 156 removed outlier: 3.580A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.820A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.666A pdb=" N ILE A 209 " --> pdb=" O VAL A 205 " (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 253 through 262 removed outlier: 3.624A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.693A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.625A pdb=" N VAL A 327 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 334 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.647A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 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 523 through 545 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.785A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 628 removed outlier: 3.868A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 609 " --> pdb=" O TRP A 605 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.637A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.849A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.910A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 794 through 818 removed outlier: 3.650A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.579A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 removed outlier: 3.891A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 949 removed outlier: 3.852A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 989 removed outlier: 3.512A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1031 removed outlier: 3.627A pdb=" N ALA A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.588A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.554A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.506A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.623A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.562A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 417 through 420 removed outlier: 3.679A pdb=" N ARG B 420 " --> pdb=" O GLY B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 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 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 523 through 544 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.546A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 625 removed outlier: 3.558A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 666 through 675 removed outlier: 3.509A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.566A pdb=" N SER B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.980A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 793 through 813 removed outlier: 3.515A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 127 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 156 removed outlier: 3.578A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.820A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.666A pdb=" N ILE C 209 " --> pdb=" O VAL C 205 " (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 253 through 262 removed outlier: 3.624A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.692A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.625A pdb=" N VAL C 327 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 331 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 334 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 335 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.647A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 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 523 through 545 Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.785A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 628 removed outlier: 3.868A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 609 " --> pdb=" O TRP C 605 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 660 removed outlier: 3.636A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.849A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.910A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 794 through 818 removed outlier: 3.650A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.578A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 847 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 927 removed outlier: 3.891A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 949 removed outlier: 3.853A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 989 removed outlier: 3.513A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 972 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1031 removed outlier: 3.627A pdb=" N ALA C1010 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 55 through 67 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.587A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.553A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.506A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.622A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.563A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 417 through 420 removed outlier: 3.679A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 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 514 through 516 No H-bonds generated for 'chain 'D' and resid 514 through 516' Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.546A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 625 removed outlier: 3.558A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 666 through 675 removed outlier: 3.508A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.566A pdb=" N SER D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.979A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 793 through 813 removed outlier: 3.516A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 removed outlier: 3.704A pdb=" N ILE A 12 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.052A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.509A pdb=" N GLY A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 372 through 374 Processing sheet with id= F, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.853A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.018A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 862 through 868 Processing sheet with id= J, first strand: chain 'B' and resid 45 through 50 removed outlier: 7.024A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.227A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.521A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.685A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.007A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 42 through 50 removed outlier: 3.705A pdb=" N ILE C 12 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= S, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.052A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.501A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 372 through 374 Processing sheet with id= V, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= W, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.853A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.019A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 862 through 868 Processing sheet with id= Z, first strand: chain 'D' and resid 45 through 50 removed outlier: 7.024A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.227A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.521A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AD, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AE, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.685A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.007A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3291 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: 10.27 Time building geometry restraints manager: 12.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 8 1.16 - 1.33: 7169 1.33 - 1.50: 11897 1.50 - 1.67: 9757 1.67 - 1.85: 249 Bond restraints: 29080 Sorted by residual: bond pdb=" C14 CLR D1103 " pdb=" C8 CLR D1103 " ideal model delta sigma weight residual 1.519 0.984 0.535 2.00e-02 2.50e+03 7.14e+02 bond pdb=" C14 CLR B1103 " pdb=" C8 CLR B1103 " ideal model delta sigma weight residual 1.519 0.985 0.534 2.00e-02 2.50e+03 7.12e+02 bond pdb=" C11 CLR D1103 " pdb=" C12 CLR D1103 " ideal model delta sigma weight residual 1.531 1.098 0.433 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C11 CLR B1103 " pdb=" C12 CLR B1103 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C7 CLR B1103 " pdb=" C8 CLR B1103 " ideal model delta sigma weight residual 1.525 1.209 0.316 2.00e-02 2.50e+03 2.49e+02 ... (remaining 29075 not shown) Histogram of bond angle deviations from ideal: 86.71 - 104.54: 363 104.54 - 122.37: 34915 122.37 - 140.20: 3962 140.20 - 158.03: 0 158.03 - 175.86: 4 Bond angle restraints: 39244 Sorted by residual: angle pdb=" C14 CLR D1103 " pdb=" C13 CLR D1103 " pdb=" C18 CLR D1103 " ideal model delta sigma weight residual 112.24 87.70 24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" C12 CLR B1103 " pdb=" C13 CLR B1103 " pdb=" C18 CLR B1103 " ideal model delta sigma weight residual 111.01 86.71 24.30 3.00e+00 1.11e-01 6.56e+01 angle pdb=" C12 CLR D1103 " pdb=" C13 CLR D1103 " pdb=" C18 CLR D1103 " ideal model delta sigma weight residual 111.01 87.49 23.52 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C14 CLR B1103 " pdb=" C13 CLR B1103 " pdb=" C18 CLR B1103 " ideal model delta sigma weight residual 112.24 88.76 23.48 3.00e+00 1.11e-01 6.13e+01 angle pdb=" N VAL B 165 " pdb=" CA VAL B 165 " pdb=" C VAL B 165 " ideal model delta sigma weight residual 112.43 106.02 6.41 9.20e-01 1.18e+00 4.86e+01 ... (remaining 39239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 16756 34.81 - 69.61: 328 69.61 - 104.42: 21 104.42 - 139.22: 7 139.22 - 174.03: 6 Dihedral angle restraints: 17118 sinusoidal: 7008 harmonic: 10110 Sorted by residual: dihedral pdb=" CA LYS A 506 " pdb=" C LYS A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta harmonic sigma weight residual -180.00 -134.87 -45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CA LYS C 506 " pdb=" C LYS C 506 " pdb=" N PRO C 507 " pdb=" CA PRO C 507 " ideal model delta harmonic sigma weight residual -180.00 -134.90 -45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA SER D 139 " pdb=" C SER D 139 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " ideal model delta harmonic sigma weight residual 180.00 141.40 38.60 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 17115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.021: 4278 1.021 - 2.041: 2 2.041 - 3.062: 2 3.062 - 4.082: 0 4.082 - 5.103: 4 Chirality restraints: 4286 Sorted by residual: chirality pdb=" C17 CLR D1103 " pdb=" C13 CLR D1103 " pdb=" C16 CLR D1103 " pdb=" C20 CLR D1103 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C17 CLR B1103 " pdb=" C13 CLR B1103 " pdb=" C16 CLR B1103 " pdb=" C20 CLR B1103 " both_signs ideal model delta sigma weight residual False 2.55 -2.53 5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C9 CLR B1103 " pdb=" C10 CLR B1103 " pdb=" C11 CLR B1103 " pdb=" C8 CLR B1103 " both_signs ideal model delta sigma weight residual False -2.45 2.40 -4.85 2.00e-01 2.50e+01 5.88e+02 ... (remaining 4283 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 6ZP C1101 " 0.030 2.00e-02 2.50e+03 2.23e-02 1.12e+01 pdb=" C03 6ZP C1101 " 0.021 2.00e-02 2.50e+03 pdb=" C04 6ZP C1101 " 0.018 2.00e-02 2.50e+03 pdb=" C05 6ZP C1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP C1101 " -0.021 2.00e-02 2.50e+03 pdb=" C07 6ZP C1101 " -0.011 2.00e-02 2.50e+03 pdb=" C08 6ZP C1101 " 0.001 2.00e-02 2.50e+03 pdb=" C09 6ZP C1101 " 0.010 2.00e-02 2.50e+03 pdb=" N01 6ZP C1101 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP A1101 " -0.030 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" C03 6ZP A1101 " -0.020 2.00e-02 2.50e+03 pdb=" C04 6ZP A1101 " -0.018 2.00e-02 2.50e+03 pdb=" C05 6ZP A1101 " 0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP A1101 " 0.021 2.00e-02 2.50e+03 pdb=" C07 6ZP A1101 " 0.010 2.00e-02 2.50e+03 pdb=" C08 6ZP A1101 " -0.002 2.00e-02 2.50e+03 pdb=" C09 6ZP A1101 " -0.010 2.00e-02 2.50e+03 pdb=" N01 6ZP A1101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP B1101 " -0.029 2.00e-02 2.50e+03 2.15e-02 1.04e+01 pdb=" C03 6ZP B1101 " -0.018 2.00e-02 2.50e+03 pdb=" C04 6ZP B1101 " -0.014 2.00e-02 2.50e+03 pdb=" C05 6ZP B1101 " -0.002 2.00e-02 2.50e+03 pdb=" C06 6ZP B1101 " 0.016 2.00e-02 2.50e+03 pdb=" C07 6ZP B1101 " 0.019 2.00e-02 2.50e+03 pdb=" C08 6ZP B1101 " 0.003 2.00e-02 2.50e+03 pdb=" C09 6ZP B1101 " -0.017 2.00e-02 2.50e+03 pdb=" N01 6ZP B1101 " 0.043 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7183 2.78 - 3.31: 25004 3.31 - 3.84: 47191 3.84 - 4.37: 59321 4.37 - 4.90: 98860 Nonbonded interactions: 237559 Sorted by model distance: nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D1201 " model vdw 2.255 2.440 nonbonded pdb=" OE1 GLN B 586 " pdb=" O HOH B1201 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR A 533 " pdb=" O LEU A 577 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR C 533 " pdb=" O LEU C 577 " model vdw 2.297 2.440 nonbonded pdb=" O VAL C 52 " pdb=" OG SER C 81 " model vdw 2.300 2.440 ... (remaining 237554 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' and (resid 10 through 1034 or resid 1101 through 1106)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 18.490 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 79.030 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.180 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.016 0.535 29080 Z= 1.012 Angle : 1.433 24.538 39244 Z= 0.748 Chirality : 0.181 5.103 4286 Planarity : 0.007 0.075 4878 Dihedral : 13.881 174.028 10632 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.12 % Favored : 92.19 % Rotamer: Outliers : 1.33 % Allowed : 5.07 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.24 % 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: -4.85 (0.11), residues: 3482 helix: -3.66 (0.08), residues: 1648 sheet: -1.90 (0.23), residues: 422 loop : -2.85 (0.13), residues: 1412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 447 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 10 residues processed: 484 average time/residue: 1.5129 time to fit residues: 853.4385 Evaluate side-chains 270 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 3.209 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 4.4296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 317 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS A 274 HIS A 318 ASN A 344 ASN A 569 ASN A 726 ASN A 747 ASN A 947 ASN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 46 HIS B 54 ASN B 164 ASN B 167 ASN B 214 HIS B 318 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 412 HIS B 508 GLN B 569 ASN B 747 ASN C 10 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 298 ASN C 344 ASN C 569 ASN C 586 GLN C 726 ASN C 747 ASN C 947 ASN C 950 HIS ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN C 990 ASN D 46 HIS D 54 ASN D 60 ASN D 164 ASN D 214 HIS D 224 ASN D 318 ASN D 337 GLN D 344 ASN D 359 ASN D 412 HIS D 569 ASN D 575 ASN D 747 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29080 Z= 0.206 Angle : 0.748 33.240 39244 Z= 0.362 Chirality : 0.059 1.902 4286 Planarity : 0.005 0.062 4878 Dihedral : 13.313 173.669 4152 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.31 % Favored : 94.23 % Rotamer: Outliers : 2.90 % Allowed : 10.31 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -2.69 (0.12), residues: 3482 helix: -1.25 (0.11), residues: 1644 sheet: -1.57 (0.22), residues: 456 loop : -2.40 (0.15), residues: 1382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 317 time to evaluate : 3.529 Fit side-chains revert: symmetry clash outliers start: 87 outliers final: 28 residues processed: 380 average time/residue: 1.4312 time to fit residues: 640.8121 Evaluate side-chains 283 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 3.167 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.6106 time to fit residues: 6.7115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 264 optimal weight: 0.0070 chunk 216 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 255 optimal weight: 20.0000 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 224 ASN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 224 ASN B 337 GLN B 344 ASN B 709 ASN C 13 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN D 709 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29080 Z= 0.206 Angle : 0.702 33.221 39244 Z= 0.330 Chirality : 0.057 1.793 4286 Planarity : 0.004 0.055 4878 Dihedral : 12.748 172.016 4152 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.69 % Favored : 94.00 % Rotamer: Outliers : 3.10 % Allowed : 12.21 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.09 % 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: -1.56 (0.14), residues: 3482 helix: 0.00 (0.12), residues: 1652 sheet: -1.41 (0.22), residues: 466 loop : -2.14 (0.16), residues: 1364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 277 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 43 residues processed: 347 average time/residue: 1.3618 time to fit residues: 561.1376 Evaluate side-chains 290 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 7 average time/residue: 0.6675 time to fit residues: 10.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 0.2980 chunk 239 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 213 optimal weight: 0.7980 chunk 319 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 302 optimal weight: 0.0980 chunk 91 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 575 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29080 Z= 0.184 Angle : 0.676 32.923 39244 Z= 0.315 Chirality : 0.057 1.807 4286 Planarity : 0.004 0.052 4878 Dihedral : 12.343 170.990 4152 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 3.07 % Allowed : 12.98 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.88 (0.14), residues: 3482 helix: 0.74 (0.13), residues: 1648 sheet: -1.27 (0.23), residues: 466 loop : -1.97 (0.16), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 266 time to evaluate : 3.294 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 47 residues processed: 336 average time/residue: 1.3774 time to fit residues: 549.0343 Evaluate side-chains 288 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 3.493 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 5 average time/residue: 0.5034 time to fit residues: 8.2745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 288 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 303 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 412 HIS B 709 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 575 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29080 Z= 0.276 Angle : 0.718 33.213 39244 Z= 0.334 Chirality : 0.058 1.779 4286 Planarity : 0.004 0.054 4878 Dihedral : 12.259 169.880 4152 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.97 % Favored : 93.74 % Rotamer: Outliers : 3.30 % Allowed : 13.61 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.77 (0.14), residues: 3482 helix: 0.82 (0.13), residues: 1652 sheet: -1.20 (0.23), residues: 466 loop : -1.92 (0.16), residues: 1364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 246 time to evaluate : 3.880 Fit side-chains revert: symmetry clash outliers start: 99 outliers final: 49 residues processed: 319 average time/residue: 1.3005 time to fit residues: 496.2682 Evaluate side-chains 278 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 39 residues processed: 11 average time/residue: 0.5001 time to fit residues: 12.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 338 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- 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 298 ASN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 575 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29080 Z= 0.178 Angle : 0.674 32.809 39244 Z= 0.309 Chirality : 0.057 1.811 4286 Planarity : 0.004 0.050 4878 Dihedral : 11.942 170.362 4152 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.40 % Favored : 94.37 % Rotamer: Outliers : 2.60 % Allowed : 14.38 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.45 (0.14), residues: 3482 helix: 1.17 (0.13), residues: 1648 sheet: -1.03 (0.24), residues: 466 loop : -1.88 (0.16), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 248 time to evaluate : 3.315 Fit side-chains revert: symmetry clash outliers start: 78 outliers final: 46 residues processed: 311 average time/residue: 1.2809 time to fit residues: 478.1032 Evaluate side-chains 283 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 3.017 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 42 residues processed: 5 average time/residue: 1.1077 time to fit residues: 11.3274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 575 ASN D 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29080 Z= 0.269 Angle : 0.714 33.121 39244 Z= 0.331 Chirality : 0.058 1.786 4286 Planarity : 0.004 0.053 4878 Dihedral : 11.965 170.391 4152 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.00 % Favored : 93.77 % Rotamer: Outliers : 2.80 % Allowed : 14.58 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.52 (0.14), residues: 3482 helix: 1.07 (0.13), residues: 1658 sheet: -1.04 (0.23), residues: 494 loop : -1.89 (0.16), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 237 time to evaluate : 3.236 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 52 residues processed: 305 average time/residue: 1.3069 time to fit residues: 479.6043 Evaluate side-chains 283 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 48 residues processed: 6 average time/residue: 0.5033 time to fit residues: 8.9620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 0.0980 chunk 134 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 101 optimal weight: 0.0020 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 265 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 412 HIS D 575 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29080 Z= 0.155 Angle : 0.665 32.512 39244 Z= 0.303 Chirality : 0.056 1.825 4286 Planarity : 0.003 0.048 4878 Dihedral : 11.651 170.895 4152 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 2.47 % Allowed : 15.04 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.19 (0.15), residues: 3482 helix: 1.44 (0.13), residues: 1648 sheet: -0.96 (0.24), residues: 466 loop : -1.80 (0.16), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 238 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 50 residues processed: 297 average time/residue: 1.2488 time to fit residues: 444.5724 Evaluate side-chains 279 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 3.131 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 5 average time/residue: 0.5011 time to fit residues: 8.0586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 294 optimal weight: 0.0030 chunk 314 optimal weight: 7.9990 chunk 189 optimal weight: 0.2980 chunk 136 optimal weight: 0.6980 chunk 246 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 313 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29080 Z= 0.155 Angle : 0.670 32.242 39244 Z= 0.304 Chirality : 0.056 1.832 4286 Planarity : 0.003 0.049 4878 Dihedral : 11.331 170.938 4152 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.60 % Favored : 94.23 % Rotamer: Outliers : 2.27 % Allowed : 15.54 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.04 (0.15), residues: 3482 helix: 1.57 (0.13), residues: 1652 sheet: -0.92 (0.23), residues: 482 loop : -1.75 (0.16), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 240 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 47 residues processed: 297 average time/residue: 1.3188 time to fit residues: 471.5867 Evaluate side-chains 283 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 3.157 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 2 average time/residue: 0.3755 time to fit residues: 5.6117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 5.9990 chunk 332 optimal weight: 0.0370 chunk 202 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 348 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29080 Z= 0.196 Angle : 0.689 32.441 39244 Z= 0.314 Chirality : 0.057 1.821 4286 Planarity : 0.004 0.049 4878 Dihedral : 11.176 171.077 4152 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.69 % Favored : 94.14 % Rotamer: Outliers : 1.63 % Allowed : 16.41 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.07 (0.15), residues: 3482 helix: 1.51 (0.13), residues: 1652 sheet: -0.87 (0.23), residues: 480 loop : -1.74 (0.16), residues: 1350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 240 time to evaluate : 2.952 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 47 residues processed: 286 average time/residue: 1.3564 time to fit residues: 465.7573 Evaluate side-chains 279 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 3.218 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 2 average time/residue: 0.3363 time to fit residues: 5.5918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 285 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.170540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121403 restraints weight = 37057.540| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.23 r_work: 0.3246 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29080 Z= 0.200 Angle : 0.694 32.414 39244 Z= 0.317 Chirality : 0.057 1.824 4286 Planarity : 0.003 0.049 4878 Dihedral : 11.042 171.260 4152 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.63 % Favored : 94.20 % Rotamer: Outliers : 1.93 % Allowed : 16.24 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.02 (0.15), residues: 3482 helix: 1.54 (0.13), residues: 1650 sheet: -0.83 (0.24), residues: 466 loop : -1.69 (0.16), residues: 1366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10048.46 seconds wall clock time: 180 minutes 46.70 seconds (10846.70 seconds total)