Starting phenix.real_space_refine on Tue Dec 31 22:16:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sth_25428/12_2024/7sth_25428_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sth_25428/12_2024/7sth_25428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sth_25428/12_2024/7sth_25428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sth_25428/12_2024/7sth_25428.map" model { file = "/net/cci-nas-00/data/ceres_data/7sth_25428/12_2024/7sth_25428_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sth_25428/12_2024/7sth_25428_neut.cif" } resolution = 3.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 8898 2.51 5 N 2402 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14010 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "B" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 7.94, per 1000 atoms: 0.57 Number of scatterers: 14010 At special positions: 0 Unit cell: (139.32, 113.4, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 2598 8.00 N 2402 7.00 C 8898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 861 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 796 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 861 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 796 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 33 sheets defined 16.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 23' Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.939A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.737A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.575A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.653A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.544A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.900A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 Processing helix chain 'A' and resid 864 through 871 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.916A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 23' Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.991A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.712A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.569A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.600A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.661A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 638 through 644 removed outlier: 3.682A pdb=" N LEU B 644 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 715 Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.776A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.610A pdb=" N LEU C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.773A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 68 through 72 removed outlier: 4.104A pdb=" N GLU D 72 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.522A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.689A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.625A pdb=" N HIS A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254 removed outlier: 6.920A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.866A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.560A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 599 through 607 removed outlier: 5.931A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 634 through 635 removed outlier: 3.762A pdb=" N GLY A 779 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 630 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 634 through 635 removed outlier: 3.762A pdb=" N GLY A 779 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 820 through 823 Processing sheet with id=AB8, first strand: chain 'A' and resid 858 through 863 removed outlier: 6.850A pdb=" N THR A 890 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 846 " --> pdb=" O ARG A 888 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 888 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 848 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A 886 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR A 850 " --> pdb=" O SER A 884 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER A 884 " --> pdb=" O TYR A 850 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG A 852 " --> pdb=" O ASN A 882 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A 882 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.739A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL B 94 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU B 120 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 96 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASN B 122 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.695A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.630A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 232 removed outlier: 3.633A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.897A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC8, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.865A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.592A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 599 through 604 removed outlier: 5.570A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 760 through 763 removed outlier: 3.869A pdb=" N VAL B 630 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 820 through 823 Processing sheet with id=AD6, first strand: chain 'B' and resid 858 through 863 removed outlier: 3.885A pdb=" N LEU B 845 " --> pdb=" O THR B 890 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 873 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: 5.74 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4583 1.34 - 1.46: 3384 1.46 - 1.58: 6249 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14352 Sorted by residual: bond pdb=" C CYS A 686 " pdb=" N PRO A 687 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.19e-02 7.06e+03 1.82e+00 bond pdb=" CA ASP B 690 " pdb=" C ASP B 690 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.28e-02 6.10e+03 1.49e+00 bond pdb=" CA THR B 689 " pdb=" CB THR B 689 " ideal model delta sigma weight residual 1.524 1.540 -0.017 1.41e-02 5.03e+03 1.39e+00 bond pdb=" CA VAL A 158 " pdb=" CB VAL A 158 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.34e-02 5.57e+03 1.21e+00 bond pdb=" N SER A 691 " pdb=" CA SER A 691 " ideal model delta sigma weight residual 1.459 1.447 0.013 1.20e-02 6.94e+03 1.10e+00 ... (remaining 14347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 18893 1.42 - 2.85: 460 2.85 - 4.27: 84 4.27 - 5.69: 9 5.69 - 7.12: 8 Bond angle restraints: 19454 Sorted by residual: angle pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 121.54 128.66 -7.12 1.91e+00 2.74e-01 1.39e+01 angle pdb=" C THR A 578 " pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" N PHE A 503 " ideal model delta sigma weight residual 114.23 116.91 -2.68 8.80e-01 1.29e+00 9.27e+00 angle pdb=" OG1 THR B 689 " pdb=" CB THR B 689 " pdb=" CG2 THR B 689 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.90e+00 angle pdb=" OG1 THR A 689 " pdb=" CB THR A 689 " pdb=" CG2 THR A 689 " ideal model delta sigma weight residual 109.30 103.36 5.94 2.00e+00 2.50e-01 8.83e+00 ... (remaining 19449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 7785 17.24 - 34.49: 733 34.49 - 51.73: 142 51.73 - 68.97: 32 68.97 - 86.21: 14 Dihedral angle restraints: 8706 sinusoidal: 3634 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -143.08 57.08 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -142.34 56.34 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 147.72 -54.72 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 8703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1351 0.033 - 0.067: 490 0.067 - 0.100: 163 0.100 - 0.133: 105 0.133 - 0.166: 3 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CB THR A 689 " pdb=" CA THR A 689 " pdb=" OG1 THR A 689 " pdb=" CG2 THR A 689 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB THR B 689 " pdb=" CA THR B 689 " pdb=" OG1 THR B 689 " pdb=" CG2 THR B 689 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ILE A 564 " pdb=" N ILE A 564 " pdb=" C ILE A 564 " pdb=" CB ILE A 564 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2109 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 578 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C THR B 578 " 0.044 2.00e-02 2.50e+03 pdb=" O THR B 578 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 579 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 578 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C THR A 578 " -0.041 2.00e-02 2.50e+03 pdb=" O THR A 578 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 579 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 835 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 836 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 836 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 836 " 0.020 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1097 2.74 - 3.28: 14060 3.28 - 3.82: 22516 3.82 - 4.36: 26993 4.36 - 4.90: 45996 Nonbonded interactions: 110662 Sorted by model distance: nonbonded pdb=" OD2 ASP A 499 " pdb=" OH TYR A 579 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU A 699 " pdb=" OH TYR B 144 " model vdw 2.210 3.040 nonbonded pdb=" O PRO B 77 " pdb=" ND2 ASN B 108 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU B 699 " model vdw 2.222 3.040 nonbonded pdb=" O GLU A 825 " pdb=" OH TYR A 909 " model vdw 2.236 3.040 ... (remaining 110657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.260 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.003 0.034 14352 Z= 0.194 Angle : 0.556 7.117 19454 Z= 0.298 Chirality : 0.044 0.166 2112 Planarity : 0.003 0.036 2514 Dihedral : 13.675 86.213 5310 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.47 % Favored : 92.35 % Rotamer: Outliers : 0.38 % Allowed : 0.44 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1700 helix: -0.30 (0.36), residues: 222 sheet: -0.21 (0.29), residues: 348 loop : -1.26 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 412 HIS 0.004 0.001 HIS A 830 PHE 0.018 0.001 PHE B 706 TYR 0.020 0.001 TYR B 579 ARG 0.007 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 646 TYR cc_start: 0.5889 (m-10) cc_final: 0.5641 (m-80) REVERT: B 646 TYR cc_start: 0.5846 (m-10) cc_final: 0.5284 (m-80) REVERT: B 807 MET cc_start: 0.8326 (mmp) cc_final: 0.8009 (mmm) REVERT: B 845 LEU cc_start: 0.9207 (pt) cc_final: 0.9001 (pp) outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 0.2600 time to fit residues: 31.5450 Evaluate side-chains 60 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain B residue 686 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 470 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 692 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 14352 Z= 0.595 Angle : 0.735 7.212 19454 Z= 0.380 Chirality : 0.050 0.196 2112 Planarity : 0.005 0.037 2514 Dihedral : 5.229 41.679 1896 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.71 % Favored : 91.24 % Rotamer: Outliers : 0.76 % Allowed : 7.59 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.21), residues: 1700 helix: -0.40 (0.35), residues: 234 sheet: -0.30 (0.29), residues: 352 loop : -1.39 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 412 HIS 0.007 0.001 HIS A 440 PHE 0.021 0.002 PHE A 381 TYR 0.019 0.002 TYR B 507 ARG 0.005 0.001 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8024 (tpt) cc_final: 0.7786 (tpt) REVERT: A 646 TYR cc_start: 0.6113 (m-10) cc_final: 0.5612 (m-80) REVERT: A 898 TRP cc_start: 0.8816 (m100) cc_final: 0.8546 (m100) REVERT: B 646 TYR cc_start: 0.5981 (m-10) cc_final: 0.5461 (m-80) REVERT: B 807 MET cc_start: 0.8453 (mmp) cc_final: 0.8227 (mmm) REVERT: B 898 TRP cc_start: 0.8566 (m100) cc_final: 0.8263 (m100) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.2232 time to fit residues: 25.3565 Evaluate side-chains 60 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 905 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.0770 chunk 48 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 156 optimal weight: 40.0000 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 0.2980 chunk 155 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 462 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14352 Z= 0.155 Angle : 0.561 10.271 19454 Z= 0.291 Chirality : 0.044 0.199 2112 Planarity : 0.004 0.035 2514 Dihedral : 4.751 44.624 1895 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 0.82 % Allowed : 9.99 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1700 helix: -0.10 (0.37), residues: 224 sheet: 0.16 (0.31), residues: 328 loop : -1.21 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 833 HIS 0.007 0.001 HIS A 830 PHE 0.022 0.001 PHE A 706 TYR 0.016 0.001 TYR A 579 ARG 0.004 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6097 (m-10) cc_final: 0.5628 (m-80) REVERT: A 898 TRP cc_start: 0.8741 (m100) cc_final: 0.8442 (m100) REVERT: B 442 MET cc_start: 0.9064 (tpp) cc_final: 0.8787 (tpp) REVERT: B 646 TYR cc_start: 0.5932 (m-10) cc_final: 0.5471 (m-80) REVERT: B 898 TRP cc_start: 0.8592 (m100) cc_final: 0.8135 (m100) REVERT: D 70 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7808 (pm20) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.2147 time to fit residues: 26.4917 Evaluate side-chains 65 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain D residue 70 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 14352 Z= 0.561 Angle : 0.694 7.870 19454 Z= 0.356 Chirality : 0.048 0.213 2112 Planarity : 0.004 0.036 2514 Dihedral : 5.176 43.976 1895 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.82 % Favored : 91.12 % Rotamer: Outliers : 1.14 % Allowed : 13.15 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1700 helix: -0.40 (0.36), residues: 236 sheet: -0.22 (0.30), residues: 344 loop : -1.33 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 833 HIS 0.007 0.001 HIS B 830 PHE 0.021 0.002 PHE B 565 TYR 0.020 0.002 TYR B 507 ARG 0.004 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6283 (m-10) cc_final: 0.5684 (m-80) REVERT: A 898 TRP cc_start: 0.8873 (m100) cc_final: 0.8559 (m100) REVERT: B 646 TYR cc_start: 0.5955 (m-10) cc_final: 0.5437 (m-80) REVERT: B 807 MET cc_start: 0.8540 (mmm) cc_final: 0.8301 (mmm) REVERT: B 898 TRP cc_start: 0.8709 (m100) cc_final: 0.8354 (m100) REVERT: C 70 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8206 (pm20) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 0.2157 time to fit residues: 25.7390 Evaluate side-chains 67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14352 Z= 0.189 Angle : 0.565 11.788 19454 Z= 0.290 Chirality : 0.044 0.198 2112 Planarity : 0.003 0.034 2514 Dihedral : 4.816 44.869 1895 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 1.14 % Allowed : 14.41 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1700 helix: -0.13 (0.37), residues: 224 sheet: 0.10 (0.31), residues: 328 loop : -1.23 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 833 HIS 0.004 0.001 HIS B 859 PHE 0.022 0.001 PHE B 706 TYR 0.015 0.001 TYR A 507 ARG 0.003 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6117 (m-10) cc_final: 0.5515 (m-80) REVERT: A 898 TRP cc_start: 0.8801 (m100) cc_final: 0.8513 (m100) REVERT: B 442 MET cc_start: 0.9184 (mmm) cc_final: 0.8782 (tpp) REVERT: B 646 TYR cc_start: 0.5892 (m-10) cc_final: 0.5383 (m-80) REVERT: B 807 MET cc_start: 0.8644 (mmm) cc_final: 0.8390 (mmm) REVERT: B 898 TRP cc_start: 0.8640 (m100) cc_final: 0.8255 (m100) REVERT: D 70 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7614 (pm20) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.2168 time to fit residues: 28.2035 Evaluate side-chains 68 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain D residue 70 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.0870 chunk 149 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14352 Z= 0.179 Angle : 0.543 8.566 19454 Z= 0.280 Chirality : 0.043 0.205 2112 Planarity : 0.003 0.035 2514 Dihedral : 4.665 46.232 1895 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 1.52 % Allowed : 14.85 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1700 helix: -0.20 (0.37), residues: 222 sheet: 0.15 (0.31), residues: 328 loop : -1.15 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 833 HIS 0.006 0.001 HIS A 830 PHE 0.020 0.001 PHE B 706 TYR 0.017 0.001 TYR B 507 ARG 0.002 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6193 (m-10) cc_final: 0.5626 (m-80) REVERT: A 898 TRP cc_start: 0.8814 (m100) cc_final: 0.8535 (m100) REVERT: B 646 TYR cc_start: 0.5971 (m-10) cc_final: 0.5431 (m-80) REVERT: B 807 MET cc_start: 0.8744 (mmm) cc_final: 0.8489 (mmm) REVERT: B 898 TRP cc_start: 0.8597 (m100) cc_final: 0.8223 (m100) REVERT: D 70 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7496 (pm20) outliers start: 24 outliers final: 15 residues processed: 89 average time/residue: 0.1977 time to fit residues: 30.0054 Evaluate side-chains 77 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14352 Z= 0.217 Angle : 0.551 10.161 19454 Z= 0.284 Chirality : 0.044 0.210 2112 Planarity : 0.003 0.035 2514 Dihedral : 4.629 46.864 1895 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 1.71 % Allowed : 14.98 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1700 helix: -0.39 (0.36), residues: 236 sheet: 0.17 (0.31), residues: 328 loop : -1.15 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 833 HIS 0.005 0.001 HIS A 830 PHE 0.018 0.001 PHE B 706 TYR 0.016 0.001 TYR B 507 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6262 (m-10) cc_final: 0.5723 (m-80) REVERT: A 777 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: A 898 TRP cc_start: 0.8789 (m100) cc_final: 0.8497 (m100) REVERT: B 646 TYR cc_start: 0.5921 (m-10) cc_final: 0.5412 (m-80) REVERT: B 807 MET cc_start: 0.8742 (mmm) cc_final: 0.8486 (mmm) REVERT: B 898 TRP cc_start: 0.8612 (m100) cc_final: 0.8270 (m100) outliers start: 27 outliers final: 18 residues processed: 87 average time/residue: 0.2068 time to fit residues: 30.8367 Evaluate side-chains 80 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14352 Z= 0.383 Angle : 0.619 11.116 19454 Z= 0.316 Chirality : 0.045 0.215 2112 Planarity : 0.004 0.035 2514 Dihedral : 4.855 46.477 1895 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 1.77 % Allowed : 15.04 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1700 helix: -0.41 (0.36), residues: 234 sheet: -0.11 (0.30), residues: 348 loop : -1.22 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 833 HIS 0.006 0.001 HIS B 830 PHE 0.018 0.002 PHE B 565 TYR 0.020 0.002 TYR B 507 ARG 0.003 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6371 (m-10) cc_final: 0.5790 (m-80) REVERT: A 777 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6726 (m-10) REVERT: A 898 TRP cc_start: 0.8851 (m100) cc_final: 0.8591 (m100) REVERT: B 646 TYR cc_start: 0.5982 (m-10) cc_final: 0.5356 (m-80) REVERT: B 807 MET cc_start: 0.8775 (mmm) cc_final: 0.8487 (mmm) REVERT: B 898 TRP cc_start: 0.8648 (m100) cc_final: 0.8330 (m100) REVERT: C 70 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8020 (mp10) outliers start: 28 outliers final: 18 residues processed: 88 average time/residue: 0.2042 time to fit residues: 30.4366 Evaluate side-chains 74 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14352 Z= 0.442 Angle : 0.652 11.351 19454 Z= 0.334 Chirality : 0.046 0.217 2112 Planarity : 0.004 0.034 2514 Dihedral : 5.006 46.141 1895 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 1.64 % Allowed : 15.36 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1700 helix: -0.43 (0.35), residues: 234 sheet: -0.27 (0.30), residues: 350 loop : -1.25 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 833 HIS 0.006 0.001 HIS B 830 PHE 0.018 0.002 PHE A 565 TYR 0.020 0.002 TYR A 507 ARG 0.003 0.000 ARG A 888 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6341 (m-10) cc_final: 0.5796 (m-80) REVERT: A 777 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6905 (m-10) REVERT: A 898 TRP cc_start: 0.8907 (m100) cc_final: 0.8596 (m100) REVERT: B 646 TYR cc_start: 0.6096 (m-10) cc_final: 0.5364 (m-80) REVERT: B 807 MET cc_start: 0.8740 (mmm) cc_final: 0.8436 (mmm) REVERT: B 898 TRP cc_start: 0.8688 (m100) cc_final: 0.8364 (m100) outliers start: 26 outliers final: 20 residues processed: 78 average time/residue: 0.2338 time to fit residues: 30.7020 Evaluate side-chains 75 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 50.0000 chunk 136 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 0.0070 chunk 145 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14352 Z= 0.175 Angle : 0.565 11.942 19454 Z= 0.290 Chirality : 0.044 0.203 2112 Planarity : 0.003 0.034 2514 Dihedral : 4.669 46.863 1895 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 1.39 % Allowed : 15.55 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1700 helix: -0.14 (0.37), residues: 224 sheet: -0.07 (0.30), residues: 346 loop : -1.10 (0.20), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 833 HIS 0.007 0.001 HIS A 830 PHE 0.021 0.001 PHE B 706 TYR 0.016 0.001 TYR B 507 ARG 0.003 0.000 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 TYR cc_start: 0.6279 (m-10) cc_final: 0.5685 (m-80) REVERT: A 777 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6838 (m-10) REVERT: A 833 TRP cc_start: 0.3954 (p90) cc_final: 0.3615 (p-90) REVERT: A 898 TRP cc_start: 0.8820 (m100) cc_final: 0.8504 (m100) REVERT: B 646 TYR cc_start: 0.5925 (m-10) cc_final: 0.5295 (m-80) REVERT: B 807 MET cc_start: 0.8717 (mmm) cc_final: 0.8345 (mmm) REVERT: B 898 TRP cc_start: 0.8627 (m100) cc_final: 0.8303 (m100) REVERT: C 70 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: D 70 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7690 (pm20) outliers start: 22 outliers final: 18 residues processed: 83 average time/residue: 0.2194 time to fit residues: 30.0822 Evaluate side-chains 83 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 686 CYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 70 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.114548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073270 restraints weight = 36481.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.076021 restraints weight = 17756.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.077720 restraints weight = 12030.719| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 14352 Z= 0.288 Angle : 0.801 59.187 19454 Z= 0.461 Chirality : 0.045 0.312 2112 Planarity : 0.004 0.108 2514 Dihedral : 4.694 46.866 1895 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 1.26 % Allowed : 15.87 % Favored : 82.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1700 helix: -0.31 (0.36), residues: 236 sheet: -0.06 (0.30), residues: 346 loop : -1.12 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 833 HIS 0.007 0.001 HIS A 830 PHE 0.019 0.001 PHE B 706 TYR 0.016 0.001 TYR B 507 ARG 0.030 0.000 ARG B 851 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.34 seconds wall clock time: 42 minutes 49.92 seconds (2569.92 seconds total)