Starting phenix.real_space_refine on Sun Jun 15 19:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4c_41878/06_2025/8u4c_41878_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4c_41878/06_2025/8u4c_41878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4c_41878/06_2025/8u4c_41878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4c_41878/06_2025/8u4c_41878.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4c_41878/06_2025/8u4c_41878_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4c_41878/06_2025/8u4c_41878_neut.cif" } resolution = 3.6 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= 0.001 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 3510 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 120 5.16 5 C 9324 2.51 5 N 2532 2.21 5 O 2730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14706 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6610 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6610 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773} Chain breaks: 6 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "F" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Time building chain proxies: 9.88, per 1000 atoms: 0.67 Number of scatterers: 14706 At special positions: 0 Unit cell: (135, 122.04, 170.64, 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 120 16.00 O 2730 8.00 N 2532 7.00 C 9324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " 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=2.02 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 60 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 51 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 17.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.584A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.664A pdb=" N ARG A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.243A pdb=" N ASN A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.650A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.893A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 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: 3.781A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 643' Processing helix chain 'A' and resid 692 through 714 Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.580A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.663A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.250A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.657A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.900A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 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 643 removed outlier: 3.772A pdb=" N PHE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 692 through 714 removed outlier: 3.562A pdb=" N LEU B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 881 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.518A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.805A pdb=" N THR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.863A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.704A pdb=" N LEU D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.514A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.803A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 3.879A pdb=" N ASP F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 52 through 58 removed outlier: 3.675A pdb=" N LEU F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.031A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (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 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 removed outlier: 3.625A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 321 removed outlier: 9.953A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 9.953A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.053A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 486 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.551A pdb=" N LEU A 505 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.560A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 771 through 774 removed outlier: 3.666A pdb=" N GLU A 772 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 630 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 627 " --> pdb=" O CYS A 798 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 827 through 834 removed outlier: 5.092A pdb=" N GLN A 845 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 884 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 854 through 863 removed outlier: 3.724A pdb=" N GLY A 892 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 917 " --> pdb=" O GLY A 892 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 13 removed outlier: 7.031A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.624A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 9.946A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321 removed outlier: 9.946A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC7, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.001A pdb=" N ARG B 479 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 486 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.501A pdb=" N THR B 530 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 505 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.554A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 771 through 774 removed outlier: 3.604A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 834 removed outlier: 5.070A pdb=" N GLN B 845 " --> pdb=" O PRO B 829 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 854 through 863 removed outlier: 3.707A pdb=" N GLY B 892 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 917 " --> pdb=" O GLY B 892 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 861 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: 5.68 Time building geometry restraints manager: 4.40 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: 4830 1.34 - 1.46: 3439 1.46 - 1.58: 6637 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 15048 Sorted by residual: bond pdb=" C CYS A 192 " pdb=" N PRO A 193 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.33e-02 5.65e+03 3.41e+00 bond pdb=" C CYS B 192 " pdb=" N PRO B 193 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.33e-02 5.65e+03 3.11e+00 bond pdb=" CB ARG F 38 " pdb=" CG ARG F 38 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.59e-02 3.96e+03 1.15e+00 bond pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 15043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 20163 2.43 - 4.87: 180 4.87 - 7.30: 17 7.30 - 9.74: 12 9.74 - 12.17: 2 Bond angle restraints: 20374 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 113.53 108.38 5.15 9.80e-01 1.04e+00 2.77e+01 angle pdb=" CA ARG F 38 " pdb=" CB ARG F 38 " pdb=" CG ARG F 38 " ideal model delta sigma weight residual 114.10 123.50 -9.40 2.00e+00 2.50e-01 2.21e+01 angle pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " pdb=" CG ARG D 38 " ideal model delta sigma weight residual 114.10 123.12 -9.02 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CB MET B 843 " pdb=" CG MET B 843 " pdb=" SD MET B 843 " ideal model delta sigma weight residual 112.70 124.87 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB MET A 843 " pdb=" CG MET A 843 " pdb=" SD MET A 843 " ideal model delta sigma weight residual 112.70 124.32 -11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 20369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7713 17.74 - 35.48: 1094 35.48 - 53.22: 249 53.22 - 70.96: 43 70.96 - 88.70: 41 Dihedral angle restraints: 9140 sinusoidal: 3826 harmonic: 5314 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.51 84.51 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual -86.00 -163.27 77.27 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 9137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1378 0.031 - 0.061: 529 0.061 - 0.092: 168 0.092 - 0.122: 129 0.122 - 0.153: 12 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CA THR B 802 " pdb=" N THR B 802 " pdb=" C THR B 802 " pdb=" CB THR B 802 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA THR A 802 " pdb=" N THR A 802 " pdb=" C THR A 802 " pdb=" CB THR A 802 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE B 457 " pdb=" N ILE B 457 " pdb=" C ILE B 457 " pdb=" CB ILE B 457 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2213 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 632 " 0.017 2.00e-02 2.50e+03 1.53e-02 5.84e+00 pdb=" CG TRP B 632 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 632 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 632 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 632 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 632 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 632 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 911 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 912 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 912 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 912 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 911 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 912 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " -0.023 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 571 2.71 - 3.26: 14960 3.26 - 3.80: 23866 3.80 - 4.35: 28826 4.35 - 4.90: 47822 Nonbonded interactions: 116045 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.163 3.040 nonbonded pdb=" O PRO B 716 " pdb=" OH TYR D 27 " model vdw 2.183 3.040 nonbonded pdb=" O PRO A 716 " pdb=" OH TYR F 27 " model vdw 2.193 3.040 nonbonded pdb=" OG SER A 890 " pdb=" OH TYR A 894 " model vdw 2.198 3.040 ... (remaining 116040 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.341 15096 Z= 0.389 Angle : 0.609 12.171 20466 Z= 0.308 Chirality : 0.042 0.153 2216 Planarity : 0.003 0.043 2634 Dihedral : 17.057 88.702 5570 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 29.12 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.20), residues: 1782 helix: 0.44 (0.38), residues: 192 sheet: -0.35 (0.28), residues: 352 loop : -1.32 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 632 HIS 0.008 0.000 HIS A 440 PHE 0.017 0.001 PHE A 572 TYR 0.015 0.001 TYR B 374 ARG 0.004 0.000 ARG A 882 Details of bonding type rmsd hydrogen bonds : bond 0.24102 ( 314) hydrogen bonds : angle 9.18251 ( 861) SS BOND : bond 0.00246 ( 46) SS BOND : angle 0.88504 ( 92) covalent geometry : bond 0.00296 (15048) covalent geometry : angle 0.60738 (20374) Misc. bond : bond 0.31750 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.8595 (tpp) cc_final: 0.7577 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3869 time to fit residues: 36.6693 Evaluate side-chains 47 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.081808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051260 restraints weight = 63054.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052907 restraints weight = 34333.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053933 restraints weight = 24467.874| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15096 Z= 0.201 Angle : 0.630 9.616 20466 Z= 0.322 Chirality : 0.044 0.145 2216 Planarity : 0.005 0.128 2634 Dihedral : 4.435 17.463 1996 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.18 % Favored : 92.59 % Rotamer: Outliers : 2.00 % Allowed : 26.51 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.46 (0.20), residues: 1782 helix: -0.02 (0.36), residues: 200 sheet: -0.60 (0.27), residues: 364 loop : -1.31 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 632 HIS 0.005 0.001 HIS A 440 PHE 0.017 0.001 PHE B 705 TYR 0.015 0.001 TYR A 374 ARG 0.015 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 314) hydrogen bonds : angle 7.13697 ( 861) SS BOND : bond 0.00338 ( 46) SS BOND : angle 0.98152 ( 92) covalent geometry : bond 0.00461 (15048) covalent geometry : angle 0.62805 (20374) Misc. bond : bond 0.00257 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9055 (tp) REVERT: A 843 MET cc_start: 0.8969 (tpp) cc_final: 0.7911 (mmm) REVERT: B 412 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.5792 (m-90) REVERT: B 442 MET cc_start: 0.9276 (mmm) cc_final: 0.8806 (mmm) outliers start: 33 outliers final: 14 residues processed: 84 average time/residue: 0.2536 time to fit residues: 33.4493 Evaluate side-chains 65 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 27 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 156 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.081617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052307 restraints weight = 61947.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053918 restraints weight = 32952.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.054938 restraints weight = 23008.153| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15096 Z= 0.146 Angle : 0.586 9.356 20466 Z= 0.299 Chirality : 0.043 0.144 2216 Planarity : 0.005 0.143 2634 Dihedral : 5.730 162.739 1996 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.73 % Favored : 93.04 % Rotamer: Outliers : 2.85 % Allowed : 26.27 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.20), residues: 1782 helix: -0.16 (0.35), residues: 200 sheet: -0.60 (0.28), residues: 364 loop : -1.29 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 632 HIS 0.003 0.000 HIS A 440 PHE 0.017 0.001 PHE B 705 TYR 0.014 0.001 TYR A 374 ARG 0.004 0.000 ARG F 38 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 314) hydrogen bonds : angle 6.62265 ( 861) SS BOND : bond 0.00195 ( 46) SS BOND : angle 0.83278 ( 92) covalent geometry : bond 0.00337 (15048) covalent geometry : angle 0.58437 (20374) Misc. bond : bond 0.00265 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8770 (OUTLIER) cc_final: 0.5777 (m-90) REVERT: A 442 MET cc_start: 0.8738 (tpp) cc_final: 0.8271 (tpp) REVERT: A 472 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9056 (tp) REVERT: A 843 MET cc_start: 0.8925 (tpp) cc_final: 0.7814 (mmm) REVERT: B 412 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.5782 (m-90) REVERT: B 442 MET cc_start: 0.9338 (mmm) cc_final: 0.8920 (mmm) REVERT: B 567 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8772 (ptmt) REVERT: F 53 LEU cc_start: 0.9160 (tp) cc_final: 0.8951 (tt) outliers start: 47 outliers final: 24 residues processed: 103 average time/residue: 0.2550 time to fit residues: 41.1617 Evaluate side-chains 78 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.081715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052216 restraints weight = 63405.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054783 restraints weight = 37517.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.054840 restraints weight = 22013.269| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15096 Z= 0.150 Angle : 0.576 9.301 20466 Z= 0.294 Chirality : 0.043 0.153 2216 Planarity : 0.004 0.054 2634 Dihedral : 4.329 17.311 1996 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 4.00 % Allowed : 25.12 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.45 (0.20), residues: 1782 helix: -0.12 (0.35), residues: 200 sheet: -0.60 (0.28), residues: 364 loop : -1.28 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 632 HIS 0.002 0.000 HIS A 710 PHE 0.013 0.001 PHE B 506 TYR 0.047 0.001 TYR A 708 ARG 0.014 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 314) hydrogen bonds : angle 6.41507 ( 861) SS BOND : bond 0.00192 ( 46) SS BOND : angle 0.80399 ( 92) covalent geometry : bond 0.00344 (15048) covalent geometry : angle 0.57517 (20374) Misc. bond : bond 0.01361 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 55 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8797 (OUTLIER) cc_final: 0.5838 (m-90) REVERT: A 442 MET cc_start: 0.8888 (tpp) cc_final: 0.8417 (tpp) REVERT: A 472 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9066 (tp) REVERT: A 635 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (mp-120) REVERT: A 843 MET cc_start: 0.8836 (tpp) cc_final: 0.7622 (mmm) REVERT: B 412 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.5571 (m-90) REVERT: B 442 MET cc_start: 0.9346 (mmm) cc_final: 0.8815 (mmm) REVERT: B 567 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8732 (ptmt) REVERT: B 635 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8259 (mp-120) REVERT: B 843 MET cc_start: 0.8694 (tpp) cc_final: 0.8293 (tpp) REVERT: F 53 LEU cc_start: 0.9170 (tp) cc_final: 0.8935 (tt) outliers start: 66 outliers final: 35 residues processed: 117 average time/residue: 0.2622 time to fit residues: 49.0700 Evaluate side-chains 93 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 52 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.0470 chunk 145 optimal weight: 0.9980 chunk 149 optimal weight: 40.0000 chunk 58 optimal weight: 0.0270 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 overall best weight: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.081716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051737 restraints weight = 63568.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053436 restraints weight = 33586.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054520 restraints weight = 23328.826| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15096 Z= 0.133 Angle : 0.571 9.229 20466 Z= 0.290 Chirality : 0.043 0.170 2216 Planarity : 0.006 0.187 2634 Dihedral : 6.651 161.140 1996 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.62 % Favored : 93.15 % Rotamer: Outliers : 3.45 % Allowed : 26.15 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.43 (0.20), residues: 1782 helix: -0.19 (0.35), residues: 200 sheet: -0.60 (0.28), residues: 358 loop : -1.24 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 632 HIS 0.005 0.000 HIS A 185 PHE 0.027 0.001 PHE E 28 TYR 0.015 0.001 TYR A 708 ARG 0.022 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 314) hydrogen bonds : angle 6.15897 ( 861) SS BOND : bond 0.00193 ( 46) SS BOND : angle 0.80299 ( 92) covalent geometry : bond 0.00310 (15048) covalent geometry : angle 0.56999 (20374) Misc. bond : bond 0.00367 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 60 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8777 (OUTLIER) cc_final: 0.5840 (m-90) REVERT: A 442 MET cc_start: 0.8943 (tpp) cc_final: 0.8416 (tpp) REVERT: A 472 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9070 (tp) REVERT: A 582 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8163 (mttp) REVERT: A 635 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8485 (mp-120) REVERT: A 843 MET cc_start: 0.8966 (tpp) cc_final: 0.7893 (mmm) REVERT: B 223 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9162 (p) REVERT: B 412 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.5695 (m-90) REVERT: B 442 MET cc_start: 0.9349 (mmm) cc_final: 0.8880 (mmm) REVERT: B 567 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8777 (ptmt) REVERT: B 635 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8321 (mp-120) REVERT: F 53 LEU cc_start: 0.9151 (tp) cc_final: 0.8923 (tt) outliers start: 57 outliers final: 38 residues processed: 115 average time/residue: 0.2696 time to fit residues: 50.3633 Evaluate side-chains 98 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 52 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.081800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052297 restraints weight = 62359.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053962 restraints weight = 32719.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.055030 restraints weight = 22615.443| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15096 Z= 0.132 Angle : 0.574 9.321 20466 Z= 0.289 Chirality : 0.043 0.187 2216 Planarity : 0.008 0.399 2634 Dihedral : 5.071 120.571 1996 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.45 % Favored : 93.32 % Rotamer: Outliers : 3.63 % Allowed : 26.27 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.39 (0.20), residues: 1782 helix: -0.02 (0.35), residues: 198 sheet: -0.60 (0.28), residues: 358 loop : -1.23 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 632 HIS 0.004 0.000 HIS A 710 PHE 0.015 0.001 PHE A 705 TYR 0.043 0.001 TYR A 708 ARG 0.044 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 314) hydrogen bonds : angle 6.06155 ( 861) SS BOND : bond 0.00192 ( 46) SS BOND : angle 0.78253 ( 92) covalent geometry : bond 0.00301 (15048) covalent geometry : angle 0.57295 (20374) Misc. bond : bond 0.01036 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 54 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9128 (p) REVERT: A 412 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.5897 (m-90) REVERT: A 582 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8138 (mttp) REVERT: A 635 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8392 (mp-120) REVERT: A 843 MET cc_start: 0.8944 (tpp) cc_final: 0.7664 (mmm) REVERT: B 223 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9158 (p) REVERT: B 412 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.5704 (m-90) REVERT: B 442 MET cc_start: 0.9327 (mmm) cc_final: 0.8852 (mmm) REVERT: B 567 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8776 (ptmt) REVERT: B 635 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8177 (mp-120) REVERT: B 843 MET cc_start: 0.8824 (tpp) cc_final: 0.8592 (tpp) REVERT: F 53 LEU cc_start: 0.9168 (tp) cc_final: 0.8936 (tt) outliers start: 60 outliers final: 37 residues processed: 112 average time/residue: 0.2955 time to fit residues: 55.4925 Evaluate side-chains 96 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 51 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.081774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051715 restraints weight = 63289.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053412 restraints weight = 33377.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054495 restraints weight = 23285.409| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15096 Z= 0.111 Angle : 0.554 9.197 20466 Z= 0.279 Chirality : 0.043 0.179 2216 Planarity : 0.004 0.096 2634 Dihedral : 4.182 17.637 1996 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.23 % Favored : 93.55 % Rotamer: Outliers : 3.57 % Allowed : 26.03 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.20), residues: 1782 helix: 0.05 (0.36), residues: 198 sheet: -0.57 (0.28), residues: 348 loop : -1.21 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 632 HIS 0.004 0.001 HIS A 100 PHE 0.013 0.001 PHE A 705 TYR 0.024 0.001 TYR A 708 ARG 0.009 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 314) hydrogen bonds : angle 5.91892 ( 861) SS BOND : bond 0.00175 ( 46) SS BOND : angle 0.72150 ( 92) covalent geometry : bond 0.00257 (15048) covalent geometry : angle 0.55337 (20374) Misc. bond : bond 0.00207 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 52 time to evaluate : 2.329 Fit side-chains REVERT: A 223 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9116 (p) REVERT: A 412 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.5893 (m-90) REVERT: A 582 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8123 (mttp) REVERT: A 635 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8473 (mp-120) REVERT: A 843 MET cc_start: 0.8825 (tpp) cc_final: 0.7722 (mmm) REVERT: B 223 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9167 (p) REVERT: B 412 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.5661 (m-90) REVERT: B 442 MET cc_start: 0.9315 (mmm) cc_final: 0.8832 (mmm) REVERT: B 567 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8793 (ptmt) REVERT: B 635 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (mp-120) REVERT: F 53 LEU cc_start: 0.9070 (tp) cc_final: 0.8812 (tt) outliers start: 59 outliers final: 37 residues processed: 109 average time/residue: 0.2155 time to fit residues: 40.2123 Evaluate side-chains 93 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 48 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 110 optimal weight: 0.0060 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.080549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050727 restraints weight = 62006.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.052309 restraints weight = 33176.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.053306 restraints weight = 23313.797| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15096 Z= 0.186 Angle : 0.611 9.925 20466 Z= 0.302 Chirality : 0.044 0.190 2216 Planarity : 0.004 0.043 2634 Dihedral : 4.338 17.520 1996 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.82 % Rotamer: Outliers : 3.57 % Allowed : 26.09 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.46 (0.20), residues: 1782 helix: 0.22 (0.36), residues: 198 sheet: -0.79 (0.28), residues: 342 loop : -1.28 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 632 HIS 0.006 0.001 HIS A 100 PHE 0.018 0.001 PHE B 482 TYR 0.015 0.001 TYR A 708 ARG 0.007 0.000 ARG B 488 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 314) hydrogen bonds : angle 5.86169 ( 861) SS BOND : bond 0.00245 ( 46) SS BOND : angle 0.95258 ( 92) covalent geometry : bond 0.00432 (15048) covalent geometry : angle 0.60875 (20374) Misc. bond : bond 0.00244 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 49 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 223 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9153 (p) REVERT: A 412 TRP cc_start: 0.8805 (OUTLIER) cc_final: 0.6058 (m-90) REVERT: A 442 MET cc_start: 0.9027 (tpp) cc_final: 0.8446 (tpp) REVERT: A 635 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8441 (mp-120) REVERT: A 843 MET cc_start: 0.8832 (tpp) cc_final: 0.7724 (mmm) REVERT: B 223 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9172 (p) REVERT: B 412 TRP cc_start: 0.8794 (OUTLIER) cc_final: 0.5688 (m-10) REVERT: B 567 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8799 (ptmt) REVERT: B 632 TRP cc_start: 0.6894 (p90) cc_final: 0.6636 (p90) REVERT: B 635 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8266 (mp-120) REVERT: F 38 ARG cc_start: 0.7850 (tmm-80) cc_final: 0.7520 (mpt180) REVERT: F 53 LEU cc_start: 0.9148 (tp) cc_final: 0.8877 (tt) outliers start: 59 outliers final: 41 residues processed: 106 average time/residue: 0.2457 time to fit residues: 41.4926 Evaluate side-chains 95 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 47 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 0.6980 chunk 16 optimal weight: 0.0020 chunk 134 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.0970 chunk 174 optimal weight: 0.8980 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.081924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052379 restraints weight = 61283.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054051 restraints weight = 32104.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.055123 restraints weight = 22244.598| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15096 Z= 0.098 Angle : 0.571 11.125 20466 Z= 0.284 Chirality : 0.044 0.235 2216 Planarity : 0.003 0.041 2634 Dihedral : 4.193 17.803 1996 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.84 % Favored : 93.94 % Rotamer: Outliers : 2.66 % Allowed : 27.18 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.39 (0.20), residues: 1782 helix: 0.14 (0.36), residues: 198 sheet: -0.53 (0.29), residues: 332 loop : -1.28 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 632 HIS 0.006 0.001 HIS B 100 PHE 0.016 0.001 PHE A 705 TYR 0.014 0.001 TYR A 507 ARG 0.006 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 314) hydrogen bonds : angle 5.80394 ( 861) SS BOND : bond 0.00165 ( 46) SS BOND : angle 0.73895 ( 92) covalent geometry : bond 0.00222 (15048) covalent geometry : angle 0.56996 (20374) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 52 time to evaluate : 2.519 Fit side-chains REVERT: A 223 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9111 (p) REVERT: A 412 TRP cc_start: 0.8729 (OUTLIER) cc_final: 0.6007 (m-90) REVERT: A 442 MET cc_start: 0.8979 (tpp) cc_final: 0.8455 (mmm) REVERT: A 582 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8057 (mttp) REVERT: A 635 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8333 (mp-120) REVERT: A 843 MET cc_start: 0.8806 (tpp) cc_final: 0.7655 (mmm) REVERT: B 412 TRP cc_start: 0.8708 (OUTLIER) cc_final: 0.5765 (m-10) REVERT: B 442 MET cc_start: 0.9303 (mmm) cc_final: 0.8830 (mmm) REVERT: B 635 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8244 (mp-120) REVERT: F 38 ARG cc_start: 0.7834 (tmm-80) cc_final: 0.7531 (mpt180) REVERT: F 53 LEU cc_start: 0.9079 (tp) cc_final: 0.8817 (tt) outliers start: 44 outliers final: 32 residues processed: 94 average time/residue: 0.2940 time to fit residues: 45.8495 Evaluate side-chains 87 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 49 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.079870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049256 restraints weight = 64046.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.050842 restraints weight = 34604.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051857 restraints weight = 24547.270| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 15096 Z= 0.266 Angle : 0.666 11.053 20466 Z= 0.330 Chirality : 0.046 0.201 2216 Planarity : 0.009 0.393 2634 Dihedral : 5.264 123.305 1996 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 2.72 % Allowed : 27.30 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.56 (0.20), residues: 1782 helix: 0.07 (0.35), residues: 198 sheet: -0.81 (0.28), residues: 342 loop : -1.35 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 632 HIS 0.007 0.001 HIS B 100 PHE 0.023 0.002 PHE B 482 TYR 0.052 0.002 TYR B 708 ARG 0.024 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 314) hydrogen bonds : angle 5.91179 ( 861) SS BOND : bond 0.00256 ( 46) SS BOND : angle 1.06743 ( 92) covalent geometry : bond 0.00614 (15048) covalent geometry : angle 0.66397 (20374) Misc. bond : bond 0.00381 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 49 time to evaluate : 3.309 Fit side-chains REVERT: A 186 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.8928 (p) REVERT: A 223 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9167 (p) REVERT: A 412 TRP cc_start: 0.8802 (OUTLIER) cc_final: 0.6091 (m-10) REVERT: A 635 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8558 (mp-120) REVERT: A 843 MET cc_start: 0.8857 (tpp) cc_final: 0.7769 (mmm) REVERT: B 412 TRP cc_start: 0.8788 (OUTLIER) cc_final: 0.5672 (m-90) REVERT: B 482 PHE cc_start: 0.7590 (t80) cc_final: 0.7332 (t80) REVERT: B 635 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8391 (mp-120) REVERT: F 38 ARG cc_start: 0.7901 (tmm-80) cc_final: 0.7604 (mpt180) REVERT: F 53 LEU cc_start: 0.9200 (tp) cc_final: 0.8930 (tt) outliers start: 45 outliers final: 35 residues processed: 92 average time/residue: 0.3456 time to fit residues: 52.4129 Evaluate side-chains 90 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 49 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6987 > 50: distance: 34 - 40: 32.023 distance: 40 - 41: 19.664 distance: 41 - 42: 21.229 distance: 42 - 43: 41.557 distance: 42 - 44: 17.269 distance: 44 - 45: 40.072 distance: 45 - 46: 42.214 distance: 46 - 47: 41.219 distance: 46 - 48: 26.066 distance: 48 - 49: 19.130 distance: 49 - 50: 39.076 distance: 50 - 51: 39.831 distance: 50 - 56: 41.715 distance: 52 - 53: 54.984 distance: 53 - 54: 41.174 distance: 53 - 55: 54.428 distance: 56 - 57: 38.334 distance: 57 - 58: 30.687 distance: 57 - 60: 59.576 distance: 58 - 59: 20.545 distance: 58 - 64: 60.340 distance: 60 - 61: 55.599 distance: 61 - 62: 16.343 distance: 61 - 63: 56.147 distance: 64 - 65: 41.182 distance: 65 - 66: 59.438 distance: 65 - 68: 40.217 distance: 66 - 67: 60.301 distance: 66 - 72: 20.720 distance: 67 - 91: 29.809 distance: 73 - 74: 7.820 distance: 73 - 76: 17.568 distance: 74 - 75: 51.616 distance: 74 - 77: 10.305 distance: 75 - 99: 32.669 distance: 77 - 78: 36.401 distance: 78 - 79: 28.387 distance: 79 - 80: 35.806 distance: 79 - 82: 31.840 distance: 80 - 108: 32.766 distance: 82 - 83: 24.086 distance: 83 - 84: 10.157 distance: 83 - 86: 27.855 distance: 84 - 91: 18.816 distance: 85 - 113: 34.288 distance: 86 - 87: 18.842 distance: 87 - 88: 27.195 distance: 88 - 89: 22.389 distance: 88 - 90: 6.331 distance: 91 - 92: 24.055 distance: 92 - 93: 19.758 distance: 92 - 95: 7.070 distance: 93 - 94: 23.354 distance: 93 - 99: 5.346 distance: 94 - 121: 27.478 distance: 95 - 96: 13.254 distance: 96 - 98: 14.242 distance: 99 - 100: 6.190 distance: 100 - 101: 10.474 distance: 100 - 103: 5.146 distance: 101 - 102: 14.506 distance: 101 - 108: 7.174 distance: 103 - 104: 11.861 distance: 104 - 105: 5.242 distance: 105 - 106: 5.003 distance: 105 - 107: 4.002