Starting phenix.real_space_refine on Tue Jun 24 19:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zdg_11173/06_2025/6zdg_11173_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zdg_11173/06_2025/6zdg_11173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zdg_11173/06_2025/6zdg_11173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zdg_11173/06_2025/6zdg_11173.map" model { file = "/net/cci-nas-00/data/ceres_data/6zdg_11173/06_2025/6zdg_11173_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zdg_11173/06_2025/6zdg_11173_trim.cif" } resolution = 4.7 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 9210 2.51 5 N 2424 2.21 5 O 2856 1.98 5 H 13995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 28548 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "C" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "D" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "F" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.79, per 1000 atoms: 0.55 Number of scatterers: 28548 At special positions: 0 Unit cell: (146.91, 146.91, 81.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 2856 8.00 N 2424 7.00 C 9210 6.00 H 13995 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 224 " - pdb=" SG CYS L 215 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS C 215 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 224 " - pdb=" SG CYS G 215 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG D 601 " - " ASN D 343 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 42 sheets defined 10.8% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.838A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 388' Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.937A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 93 through 97 removed outlier: 3.919A pdb=" N LEU L 97 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.738A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.838A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.936A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.918A pdb=" N LEU C 97 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.737A pdb=" N LYS C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.838A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.024A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.937A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.919A pdb=" N LEU G 97 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.738A pdb=" N LYS G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.592A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 465 through 467 removed outlier: 4.315A pdb=" N TRP G 149 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.879A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 128 through 132 removed outlier: 6.214A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 128 through 132 removed outlier: 6.214A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.431A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.177A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.950A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.485A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.108A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 206 through 211 removed outlier: 4.316A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU L 155 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.591A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.879A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.430A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 4 through 7 removed outlier: 12.176A pdb=" N CYS C 23 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N THR C 74 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 12.192A pdb=" N ALA C 25 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N THR C 72 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N GLN C 27 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP C 70 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.950A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 10 through 13 removed outlier: 4.486A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.107A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 211 removed outlier: 4.315A pdb=" N TRP C 149 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 155 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.592A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.879A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 128 through 132 removed outlier: 6.215A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 159 through 162 removed outlier: 4.431A pdb=" N TYR F 202 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 7 removed outlier: 12.176A pdb=" N CYS G 23 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N THR G 74 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ALA G 25 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N THR G 72 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N GLN G 27 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP G 70 " --> pdb=" O GLN G 27 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.949A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 10 through 13 removed outlier: 4.486A pdb=" N THR G 98 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 119 removed outlier: 6.108A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1419 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: 11.37 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13995 1.03 - 1.23: 0 1.23 - 1.42: 6503 1.42 - 1.62: 8332 1.62 - 1.81: 72 Bond restraints: 28902 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C1 NAG D 601 " pdb=" O5 NAG D 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" CB PRO H 155 " pdb=" CG PRO H 155 " ideal model delta sigma weight residual 1.506 1.462 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" CB PRO B 155 " pdb=" CG PRO B 155 " ideal model delta sigma weight residual 1.506 1.462 0.044 3.90e-02 6.57e+02 1.24e+00 ... (remaining 28897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 51921 5.96 - 11.93: 0 11.93 - 17.89: 0 17.89 - 23.85: 2 23.85 - 29.82: 4 Bond angle restraints: 51927 Sorted by residual: angle pdb=" CB VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG12 VAL C 58 " ideal model delta sigma weight residual 109.00 79.18 29.82 3.00e+00 1.11e-01 9.88e+01 angle pdb="HG11 VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG12 VAL C 58 " ideal model delta sigma weight residual 110.00 80.47 29.53 3.00e+00 1.11e-01 9.69e+01 angle pdb=" CB VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG13 VAL C 58 " ideal model delta sigma weight residual 109.00 80.12 28.88 3.00e+00 1.11e-01 9.27e+01 angle pdb="HG11 VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG13 VAL C 58 " ideal model delta sigma weight residual 110.00 81.50 28.50 3.00e+00 1.11e-01 9.02e+01 angle pdb="HG12 VAL C 58 " pdb=" CG1 VAL C 58 " pdb="HG13 VAL C 58 " ideal model delta sigma weight residual 110.00 133.63 -23.63 3.00e+00 1.11e-01 6.21e+01 ... (remaining 51922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 13185 17.53 - 35.05: 545 35.05 - 52.58: 232 52.58 - 70.11: 53 70.11 - 87.63: 4 Dihedral angle restraints: 14019 sinusoidal: 7440 harmonic: 6579 Sorted by residual: dihedral pdb=" N GLN D 493 " pdb=" CA GLN D 493 " pdb=" CB GLN D 493 " pdb=" CG GLN D 493 " ideal model delta sinusoidal sigma weight residual -180.00 -122.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN A 493 " pdb=" CA GLN A 493 " pdb=" CB GLN A 493 " pdb=" CG GLN A 493 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN E 493 " pdb=" CA GLN E 493 " pdb=" CB GLN E 493 " pdb=" CG GLN E 493 " ideal model delta sinusoidal sigma weight residual -180.00 -122.34 -57.66 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 14016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1363 0.029 - 0.058: 597 0.058 - 0.088: 112 0.088 - 0.117: 148 0.117 - 0.146: 24 Chirality restraints: 2244 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE G 75 " pdb=" N ILE G 75 " pdb=" C ILE G 75 " pdb=" CB ILE G 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 2241 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO H 157 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 157 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 156 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO F 157 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 157 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 157 " -0.022 5.00e-02 4.00e+02 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1061 2.12 - 2.74: 52820 2.74 - 3.36: 79316 3.36 - 3.98: 105482 3.98 - 4.60: 161091 Nonbonded interactions: 399770 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 386 " pdb=" O LEU B 103 " model vdw 1.499 2.450 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.519 2.450 nonbonded pdb=" H ALA D 363 " pdb=" O CYS D 525 " model vdw 1.520 2.450 nonbonded pdb=" H ALA E 363 " pdb=" O CYS E 525 " model vdw 1.520 2.450 nonbonded pdb=" HZ3 LYS D 356 " pdb=" O ARG D 357 " model vdw 1.533 2.450 ... (remaining 399765 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: 0.10 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 10.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.520 Extract box with map and model: 1.140 Check model and map are aligned: 0.230 Set scattering table: 0.330 Process input model: 61.260 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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 : 0.004 0.044 14937 Z= 0.170 Angle : 0.508 6.269 20334 Z= 0.287 Chirality : 0.041 0.146 2244 Planarity : 0.003 0.044 2601 Dihedral : 9.076 58.120 5340 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.41 % Allowed : 3.52 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1860 helix: -1.71 (0.44), residues: 117 sheet: 0.56 (0.19), residues: 726 loop : -0.04 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 353 HIS 0.003 0.001 HIS C 190 PHE 0.009 0.001 PHE E 400 TYR 0.013 0.001 TYR F 95 ARG 0.003 0.001 ARG E 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 3) link_NAG-ASN : angle 1.05476 ( 9) hydrogen bonds : bond 0.21732 ( 509) hydrogen bonds : angle 8.20242 ( 1419) SS BOND : bond 0.00662 ( 27) SS BOND : angle 1.43620 ( 54) covalent geometry : bond 0.00354 (14907) covalent geometry : angle 0.50272 (20271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7432 (pp) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.4081 time to fit residues: 28.4564 Evaluate side-chains 36 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.236 Evaluate side-chains 52 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9134 (pt0) cc_final: 0.8923 (mp0) REVERT: A 342 PHE cc_start: 0.8657 (m-80) cc_final: 0.7891 (m-80) REVERT: A 357 ARG cc_start: 0.6900 (ttt-90) cc_final: 0.6691 (tpt-90) REVERT: A 369 TYR cc_start: 0.4380 (m-10) cc_final: 0.3226 (t80) REVERT: A 457 ARG cc_start: 0.9064 (ttt-90) cc_final: 0.8779 (ttt-90) REVERT: A 486 PHE cc_start: 0.8536 (t80) cc_final: 0.7922 (t80) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.3968 time to fit residues: 21.5567 Evaluate side-chains 34 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.244 Evaluate side-chains 73 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.8060 (m-80) cc_final: 0.7840 (m-80) REVERT: B 59 TYR cc_start: 0.8156 (m-80) cc_final: 0.7572 (m-80) REVERT: B 83 MET cc_start: 0.6850 (mtm) cc_final: 0.6607 (mtm) REVERT: B 98 LYS cc_start: 0.7827 (tttt) cc_final: 0.7536 (ttmm) REVERT: B 108 PHE cc_start: 0.6401 (m-10) cc_final: 0.4416 (p90) REVERT: B 113 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8620 (mm-40) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.4095 time to fit residues: 31.9585 Evaluate side-chains 55 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 74 optimal weight: 0.0570 chunk 143 optimal weight: 0.1980 chunk 55 optimal weight: 0.0030 chunk 87 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.1508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.112364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.091394 restraints weight = 16787.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.096144 restraints weight = 9301.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.099766 restraints weight = 5886.577| |-----------------------------------------------------------------------------| r_work (final): 0.3780 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103750 restraints weight = 12946.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.108536 restraints weight = 7356.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.111774 restraints weight = 4674.685| |-----------------------------------------------------------------------------| r_work (final): 0.3800 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.129683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105970 restraints weight = 14668.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.112056 restraints weight = 8051.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.116645 restraints weight = 4975.804| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.761 14937 Z= 0.952 Angle : 0.765 21.817 20334 Z= 0.487 Chirality : 0.045 0.174 2244 Planarity : 0.006 0.092 2601 Dihedral : 4.789 43.369 2115 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.56 % Allowed : 2.04 % Favored : 97.41 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1860 helix: -2.66 (0.37), residues: 135 sheet: 0.65 (0.18), residues: 756 loop : 0.19 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP H 104 HIS 0.004 0.002 HIS B 35 PHE 0.017 0.001 PHE H 130 TYR 0.016 0.001 TYR H 184 ARG 0.005 0.001 ARG C 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 3) link_NAG-ASN : angle 1.28570 ( 9) hydrogen bonds : bond 0.04042 ( 509) hydrogen bonds : angle 6.45395 ( 1419) SS BOND : bond 0.01588 ( 27) SS BOND : angle 1.59985 ( 54) covalent geometry : bond 0.01957 (14907) covalent geometry : angle 0.76150 (20271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 TYR cc_start: 0.8831 (p90) cc_final: 0.8577 (p90) REVERT: L 70 ASP cc_start: 0.8789 (m-30) cc_final: 0.8578 (m-30) REVERT: L 191 LYS cc_start: 0.7758 (tppp) cc_final: 0.7410 (tppt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2923 time to fit residues: 15.1019 Evaluate side-chains 31 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.280 Evaluate side-chains 46 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 369 TYR cc_start: 0.4022 (m-10) cc_final: 0.2422 (t80) REVERT: E 396 TYR cc_start: 0.7016 (m-10) cc_final: 0.6692 (m-10) REVERT: E 465 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7721 (tm-30) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.4372 time to fit residues: 21.2038 Evaluate side-chains 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.261 Evaluate side-chains 56 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.7510 (mmmm) cc_final: 0.7122 (ttmt) REVERT: F 156 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7519 (mt-10) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.4747 time to fit residues: 28.0948 Evaluate side-chains 49 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 158 optimal weight: 0.5980 chunk 92 optimal weight: 0.0670 chunk 123 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 98 optimal weight: 0.0270 chunk 182 optimal weight: 0.0980 chunk 5 optimal weight: 0.0030 chunk 139 optimal weight: 0.0370 overall best weight: 0.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.108457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.086363 restraints weight = 13721.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091477 restraints weight = 7339.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.095314 restraints weight = 4479.872| |-----------------------------------------------------------------------------| r_work (final): 0.3708 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.103969 restraints weight = 11021.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.108718 restraints weight = 6296.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.111890 restraints weight = 4070.678| |-----------------------------------------------------------------------------| r_work (final): 0.3851 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.129823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105123 restraints weight = 13856.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.110902 restraints weight = 7671.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.115309 restraints weight = 4778.135| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.878 14937 Z= 1.073 Angle : 1.125 25.392 20334 Z= 0.654 Chirality : 0.051 0.426 2244 Planarity : 0.008 0.083 2601 Dihedral : 5.143 43.294 2115 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.37 % Allowed : 2.22 % Favored : 97.41 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1860 helix: -3.10 (0.32), residues: 135 sheet: 0.42 (0.18), residues: 756 loop : -0.07 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.006 TRP F 104 HIS 0.015 0.003 HIS A 519 PHE 0.079 0.004 PHE D 456 TYR 0.057 0.003 TYR D 396 ARG 0.021 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 3) link_NAG-ASN : angle 1.65510 ( 9) hydrogen bonds : bond 0.05028 ( 509) hydrogen bonds : angle 6.48443 ( 1419) SS BOND : bond 0.02609 ( 27) SS BOND : angle 1.55798 ( 54) covalent geometry : bond 0.02418 (14907) covalent geometry : angle 1.12351 (20271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4017 time to fit residues: 16.7287 Evaluate side-chains 29 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.235 Evaluate side-chains 44 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 369 TYR cc_start: 0.3560 (m-10) cc_final: 0.2710 (t80) REVERT: D 414 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7955 (mm-40) REVERT: D 465 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7301 (tm-30) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.5238 time to fit residues: 24.5715 Evaluate side-chains 31 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.211 Evaluate side-chains 52 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.7396 (mmmm) cc_final: 0.7053 (ttmt) REVERT: F 156 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7517 (mt-10) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.4693 time to fit residues: 26.2460 Evaluate side-chains 48 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 168 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.110385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.087283 restraints weight = 14539.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.092672 restraints weight = 7881.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.097018 restraints weight = 4881.807| |-----------------------------------------------------------------------------| r_work (final): 0.3716 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.104830 restraints weight = 12117.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.109278 restraints weight = 7169.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.112543 restraints weight = 4769.598| |-----------------------------------------------------------------------------| r_work (final): 0.3828 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.127726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.105909 restraints weight = 13649.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.111612 restraints weight = 7221.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.115721 restraints weight = 4308.313| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.885 14937 Z= 1.012 Angle : 1.030 21.141 20334 Z= 0.611 Chirality : 0.049 0.286 2244 Planarity : 0.013 0.329 2601 Dihedral : 5.362 43.428 2115 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.37 % Allowed : 1.11 % Favored : 98.52 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1860 helix: -3.26 (0.29), residues: 135 sheet: 0.32 (0.18), residues: 756 loop : -0.24 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.007 TRP F 104 HIS 0.014 0.002 HIS D 519 PHE 0.098 0.004 PHE A 429 TYR 0.072 0.003 TYR A 396 ARG 0.032 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 3) link_NAG-ASN : angle 1.67562 ( 9) hydrogen bonds : bond 0.05015 ( 509) hydrogen bonds : angle 6.49306 ( 1419) SS BOND : bond 0.03421 ( 27) SS BOND : angle 1.52894 ( 54) covalent geometry : bond 0.02189 (14907) covalent geometry : angle 1.02795 (20271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.3821 time to fit residues: 15.6585 Evaluate side-chains 29 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.249 Evaluate side-chains 39 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 369 TYR cc_start: 0.4025 (m-10) cc_final: 0.2366 (t80) REVERT: E 406 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7412 (mt-10) REVERT: E 465 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7687 (tm-30) outliers start: 2 outliers final: 0 residues processed: 38 average time/residue: 0.4161 time to fit residues: 17.2634 Evaluate side-chains 27 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.239 Evaluate side-chains 51 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.7466 (mmmm) cc_final: 0.7125 (ttmt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.4741 time to fit residues: 26.0970 Evaluate side-chains 46 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) 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 400, 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 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) 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/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads 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: 70.0156 > 50: distance: 0 - 1: 25.038 distance: 0 - 4: 3.647 distance: 1 - 2: 37.539 distance: 1 - 5: 30.404 distance: 1 - 6: 35.733 distance: 2 - 3: 31.180 distance: 2 - 7: 12.221 distance: 7 - 8: 44.583 distance: 7 - 14: 43.315 distance: 8 - 9: 21.186 distance: 8 - 11: 3.529 distance: 8 - 15: 12.965 distance: 9 - 23: 44.672 distance: 11 - 12: 53.712 distance: 11 - 13: 68.547 distance: 11 - 16: 40.043 distance: 12 - 17: 4.757 distance: 12 - 18: 9.480 distance: 12 - 19: 5.211 distance: 13 - 20: 55.941 distance: 13 - 21: 23.484 distance: 13 - 22: 45.815 distance: 23 - 24: 11.915 distance: 24 - 25: 27.893 distance: 24 - 28: 18.331 distance: 24 - 29: 10.988 distance: 25 - 26: 47.438 distance: 25 - 30: 26.111 distance: 30 - 31: 12.026 distance: 30 - 42: 36.356 distance: 31 - 32: 21.664 distance: 31 - 34: 32.058 distance: 31 - 43: 25.833 distance: 32 - 33: 25.369 distance: 32 - 51: 46.863 distance: 34 - 35: 15.389 distance: 34 - 44: 7.124 distance: 34 - 45: 24.769 distance: 35 - 36: 25.760 distance: 35 - 37: 21.517 distance: 36 - 38: 24.236 distance: 36 - 46: 32.137 distance: 37 - 39: 25.979 distance: 37 - 47: 17.404 distance: 38 - 40: 50.212 distance: 38 - 48: 33.494 distance: 39 - 40: 21.839 distance: 39 - 49: 17.529 distance: 40 - 41: 11.722 distance: 41 - 50: 57.242 distance: 51 - 52: 24.898 distance: 51 - 60: 26.497 distance: 52 - 53: 40.012 distance: 52 - 55: 55.552 distance: 52 - 61: 23.507 distance: 53 - 54: 39.898 distance: 55 - 56: 41.176 distance: 55 - 62: 25.771 distance: 55 - 63: 11.295 distance: 56 - 57: 6.274 distance: 56 - 64: 28.779 distance: 56 - 65: 20.917 distance: 57 - 58: 21.475 distance: 57 - 59: 19.117 distance: 59 - 66: 10.627 distance: 59 - 67: 13.565 distance: 68 - 69: 23.557 distance: 68 - 74: 52.353 distance: 69 - 70: 30.826 distance: 69 - 72: 33.984 distance: 69 - 75: 16.053 distance: 70 - 71: 22.586 distance: 70 - 82: 38.016 distance: 72 - 73: 29.626 distance: 72 - 76: 26.400 distance: 72 - 77: 23.513 distance: 73 - 74: 54.181 distance: 73 - 78: 43.580 distance: 73 - 79: 31.207 distance: 74 - 80: 40.972 distance: 74 - 81: 58.231 distance: 82 - 83: 19.812 distance: 82 - 94: 21.378 distance: 83 - 84: 15.436 distance: 83 - 86: 54.347 distance: 83 - 95: 39.778 distance: 84 - 103: 38.627 distance: 86 - 87: 46.831 distance: 86 - 96: 34.822 distance: 86 - 97: 22.700 distance: 87 - 88: 25.569 distance: 87 - 89: 21.610 distance: 88 - 90: 32.461 distance: 88 - 98: 33.493 distance: 89 - 91: 29.038 distance: 89 - 99: 44.816 distance: 90 - 92: 36.364 distance: 90 - 100: 28.749 distance: 91 - 92: 18.216 distance: 91 - 101: 17.122 distance: 92 - 93: 31.898 distance: 93 - 102: 44.074 distance: 103 - 104: 20.478 distance: 103 - 114: 44.405 distance: 104 - 105: 24.612 distance: 104 - 107: 32.716 distance: 104 - 115: 5.014 distance: 105 - 106: 22.217 distance: 105 - 127: 22.711 distance: 107 - 108: 3.707 distance: 107 - 116: 36.821 distance: 107 - 117: 23.925 distance: 108 - 109: 21.685 distance: 108 - 118: 15.257 distance: 108 - 119: 19.811 distance: 109 - 110: 50.598 distance: 109 - 121: 61.866 distance: 110 - 111: 29.928 distance: 110 - 122: 59.025 distance: 111 - 112: 15.738 distance: 111 - 113: 7.307 distance: 112 - 123: 23.820 distance: 112 - 124: 24.630 distance: 113 - 125: 16.464 distance: 113 - 126: 11.327 distance: 127 - 128: 31.535 distance: 127 - 134: 20.839 distance: 128 - 129: 13.196 distance: 128 - 131: 25.406 distance: 128 - 135: 24.070 distance: 129 - 130: 31.989 distance: 129 - 143: 31.109 distance: 131 - 132: 40.913 distance: 131 - 133: 18.319 distance: 131 - 136: 44.443 distance: 132 - 137: 56.973 distance: 132 - 138: 37.306 distance: 132 - 139: 62.528 distance: 133 - 140: 11.027 distance: 133 - 141: 22.055 distance: 133 - 142: 16.907 distance: 143 - 144: 6.583 distance: 143 - 150: 33.665 distance: 144 - 145: 20.778 distance: 144 - 147: 14.145 distance: 144 - 151: 21.462 distance: 145 - 146: 3.663 distance: 147 - 148: 21.143 distance: 147 - 149: 22.298 distance: 147 - 152: 4.740 distance: 148 - 153: 11.075 distance: 148 - 154: 7.344 distance: 148 - 155: 12.609 distance: 149 - 156: 4.638 distance: 149 - 157: 7.247 distance: 149 - 158: 6.296