Starting phenix.real_space_refine on Mon Aug 25 14:37:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zdg_11173/08_2025/6zdg_11173_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zdg_11173/08_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_11173/08_2025/6zdg_11173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zdg_11173/08_2025/6zdg_11173.map" model { file = "/net/cci-nas-00/data/ceres_data/6zdg_11173/08_2025/6zdg_11173_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zdg_11173/08_2025/6zdg_11173_trim.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.11, per 1000 atoms: 0.18 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: 1.99 Conformation dependent library (CDL) restraints added in 601.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.58 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: 6.84 Time building geometry restraints manager: 3.00 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: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'L' selection = chain 'C' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'B' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'C' selection = chain 'G' } 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: 15.900 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.810 ------------------------------------------------------------------------------- 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 : 7.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG E 403 TYR 0.013 0.001 TYR F 95 PHE 0.009 0.001 PHE E 400 TRP 0.009 0.002 TRP D 353 HIS 0.003 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00354 (14907) covalent geometry : angle 0.50272 (20271) SS BOND : bond 0.00662 ( 27) SS BOND : angle 1.43620 ( 54) hydrogen bonds : bond 0.21732 ( 509) hydrogen bonds : angle 8.20242 ( 1419) link_NAG-ASN : bond 0.00014 ( 3) link_NAG-ASN : angle 1.05476 ( 9) *********************** 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 55 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 369 TYR cc_start: 0.4019 (m-10) cc_final: 0.2470 (t80) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1746 time to fit residues: 9.8603 Evaluate side-chains 31 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.093 Evaluate side-chains 71 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.091 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: H 59 TYR cc_start: 0.8150 (m-80) cc_final: 0.7652 (m-10) REVERT: H 83 MET cc_start: 0.7311 (mtm) cc_final: 0.7087 (mtm) REVERT: H 98 LYS cc_start: 0.8233 (tttt) cc_final: 0.7974 (ttmm) REVERT: H 108 PHE cc_start: 0.6487 (m-10) cc_final: 0.4280 (p90) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.1755 time to fit residues: 13.3011 Evaluate side-chains 50 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.091 Evaluate side-chains 62 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.087 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: L 71 PHE cc_start: 0.7940 (m-80) cc_final: 0.7655 (m-80) REVERT: L 117 PHE cc_start: 0.8106 (m-80) cc_final: 0.7898 (m-80) REVERT: L 123 ASP cc_start: 0.9059 (m-30) cc_final: 0.8843 (p0) REVERT: L 214 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7302 (tm-30) REVERT: L 215 CYS cc_start: 0.3894 (OUTLIER) cc_final: 0.2695 (t) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.1499 time to fit residues: 10.0007 Evaluate side-chains 40 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 ASN D 450 ASN Total number of N/Q/H flips: 2 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 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.122977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105339 restraints weight = 10944.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.109729 restraints weight = 6155.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.112811 restraints weight = 3903.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.115078 restraints weight = 2670.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.116532 restraints weight = 1904.086| |-----------------------------------------------------------------------------| r_work (final): 0.3905 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.127144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.105292 restraints weight = 13812.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.110745 restraints weight = 7277.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.114663 restraints weight = 4359.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.117621 restraints weight = 2812.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.119683 restraints weight = 1911.026| |-----------------------------------------------------------------------------| r_work (final): 0.4011 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.109655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088608 restraints weight = 15722.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.093287 restraints weight = 9314.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096808 restraints weight = 6131.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099398 restraints weight = 4282.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.101376 restraints weight = 3127.501| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.791 14937 Z= 0.955 Angle : 0.763 22.087 20334 Z= 0.490 Chirality : 0.044 0.176 2244 Planarity : 0.005 0.049 2601 Dihedral : 4.983 43.683 2115 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.56 % Allowed : 1.85 % Favored : 97.59 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.19), residues: 1860 helix: -1.82 (0.44), residues: 120 sheet: 0.56 (0.18), residues: 732 loop : -0.17 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 466 TYR 0.014 0.001 TYR B 184 PHE 0.010 0.001 PHE D 464 TRP 0.064 0.004 TRP F 104 HIS 0.002 0.001 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.02027 (14907) covalent geometry : angle 0.75893 (20271) SS BOND : bond 0.01203 ( 27) SS BOND : angle 1.69514 ( 54) hydrogen bonds : bond 0.04991 ( 509) hydrogen bonds : angle 6.74116 ( 1419) link_NAG-ASN : bond 0.00081 ( 3) link_NAG-ASN : angle 1.24023 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.076 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: D 369 TYR cc_start: 0.3920 (m-10) cc_final: 0.2955 (t80) REVERT: D 452 LEU cc_start: 0.8780 (mt) cc_final: 0.8515 (mt) REVERT: D 514 SER cc_start: 0.8197 (p) cc_final: 0.7580 (p) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.2255 time to fit residues: 12.0144 Evaluate side-chains 33 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.080 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 : 0.053 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 outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.2205 time to fit residues: 12.9502 Evaluate side-chains 46 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.086 Evaluate side-chains 40 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.088 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: L 117 PHE cc_start: 0.8065 (m-80) cc_final: 0.7815 (m-80) REVERT: L 123 ASP cc_start: 0.8965 (m-30) cc_final: 0.8757 (p0) REVERT: L 214 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7191 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1422 time to fit residues: 6.3505 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 : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 152 optimal weight: 0.0170 chunk 157 optimal weight: 0.0060 chunk 42 optimal weight: 0.1980 chunk 70 optimal weight: 0.3980 chunk 175 optimal weight: 0.0030 chunk 112 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.0442 ------------------------------------------------------------------------------- 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: F 77 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: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.122926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.105916 restraints weight = 11069.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.110171 restraints weight = 6301.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.113338 restraints weight = 4064.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.115530 restraints weight = 2762.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.117393 restraints weight = 2019.632| |-----------------------------------------------------------------------------| r_work (final): 0.3951 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.127392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.107403 restraints weight = 13657.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112808 restraints weight = 7097.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.116594 restraints weight = 4184.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.119429 restraints weight = 2659.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.121349 restraints weight = 1769.634| |-----------------------------------------------------------------------------| r_work (final): 0.4028 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.113440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.092850 restraints weight = 17965.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.097618 restraints weight = 10617.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.101274 restraints weight = 6968.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103748 restraints weight = 4814.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.105712 restraints weight = 3542.213| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.787 14937 Z= 1.009 Angle : 1.075 26.136 20334 Z= 0.633 Chirality : 0.054 0.458 2244 Planarity : 0.008 0.107 2601 Dihedral : 5.429 47.311 2115 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.74 % Allowed : 0.93 % Favored : 98.33 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.19), residues: 1860 helix: -2.51 (0.39), residues: 117 sheet: 0.41 (0.18), residues: 732 loop : -0.34 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 346 TYR 0.046 0.003 TYR A 505 PHE 0.047 0.004 PHE B 130 TRP 0.040 0.004 TRP H 104 HIS 0.015 0.003 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.02081 (14907) covalent geometry : angle 1.05655 (20271) SS BOND : bond 0.02503 ( 27) SS BOND : angle 3.91838 ( 54) hydrogen bonds : bond 0.05080 ( 509) hydrogen bonds : angle 6.66842 ( 1419) link_NAG-ASN : bond 0.00220 ( 3) link_NAG-ASN : angle 1.62372 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.118 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: D 369 TYR cc_start: 0.3633 (m-10) cc_final: 0.2859 (t80) REVERT: D 452 LEU cc_start: 0.8761 (mt) cc_final: 0.8535 (mt) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.2834 time to fit residues: 12.3538 Evaluate side-chains 37 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.091 Evaluate side-chains 53 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.061 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: F 28 THR cc_start: 0.9212 (m) cc_final: 0.8966 (m) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1819 time to fit residues: 10.3881 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 : 0.059 Evaluate side-chains 39 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.056 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 outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0946 time to fit residues: 4.1769 Evaluate side-chains 32 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 113 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.0040 chunk 176 optimal weight: 0.0970 chunk 81 optimal weight: 0.0270 chunk 14 optimal weight: 0.0270 chunk 106 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 overall best weight: 0.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 460 ASN ** 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: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106206 restraints weight = 13219.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.111116 restraints weight = 7499.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.114740 restraints weight = 4706.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.117265 restraints weight = 3175.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.119090 restraints weight = 2280.245| |-----------------------------------------------------------------------------| r_work (final): 0.3943 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.124185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.102123 restraints weight = 13353.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.107945 restraints weight = 7096.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.112084 restraints weight = 4239.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.115060 restraints weight = 2731.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.117235 restraints weight = 1861.113| |-----------------------------------------------------------------------------| r_work (final): 0.4018 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.107115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085625 restraints weight = 15838.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.090516 restraints weight = 9051.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.094417 restraints weight = 5722.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.097333 restraints weight = 3863.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099394 restraints weight = 2753.598| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.252 14937 Z= 0.492 Angle : 0.892 14.583 20334 Z= 0.510 Chirality : 0.052 0.245 2244 Planarity : 0.008 0.094 2601 Dihedral : 5.235 43.567 2115 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 1860 helix: -2.80 (0.35), residues: 117 sheet: 0.38 (0.18), residues: 744 loop : -0.45 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 403 TYR 0.048 0.003 TYR A 396 PHE 0.038 0.003 PHE D 347 TRP 0.206 0.012 TRP B 104 HIS 0.014 0.003 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.01011 (14907) covalent geometry : angle 0.87121 (20271) SS BOND : bond 0.02067 ( 27) SS BOND : angle 3.77159 ( 54) hydrogen bonds : bond 0.05012 ( 509) hydrogen bonds : angle 6.68895 ( 1419) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.65461 ( 9) *********************** 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 43 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.066 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: 0.3980 (m-10) cc_final: 0.2439 (t80) REVERT: E 453 TYR cc_start: 0.8541 (p90) cc_final: 0.7959 (p90) REVERT: E 457 ARG cc_start: 0.9015 (ttt-90) cc_final: 0.8724 (mmm-85) REVERT: E 465 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7762 (tm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1616 time to fit residues: 7.5359 Evaluate side-chains 29 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.080 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 : 0.087 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: F 59 TYR cc_start: 0.8054 (m-80) cc_final: 0.7817 (m-10) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1641 time to fit residues: 9.0573 Evaluate side-chains 45 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.053 Evaluate side-chains 36 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.066 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: C 117 PHE cc_start: 0.7609 (m-80) cc_final: 0.7366 (m-80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0873 time to fit residues: 3.7522 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 : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2626 > 50: distance: 0 - 1: 13.702 distance: 0 - 18: 13.715 distance: 18 - 19: 12.304 distance: 18 - 27: 3.743 distance: 19 - 20: 17.377 distance: 19 - 22: 3.736 distance: 19 - 28: 16.178 distance: 20 - 21: 15.254 distance: 20 - 35: 15.664 distance: 22 - 23: 19.530 distance: 22 - 29: 20.101 distance: 22 - 30: 14.422 distance: 23 - 24: 15.059 distance: 23 - 31: 18.298 distance: 23 - 32: 18.258 distance: 24 - 25: 21.814 distance: 24 - 26: 22.826 distance: 26 - 33: 13.225 distance: 26 - 34: 14.110 distance: 35 - 36: 8.557 distance: 35 - 41: 23.430 distance: 36 - 37: 11.874 distance: 36 - 39: 10.414 distance: 36 - 42: 18.227 distance: 37 - 38: 14.843 distance: 37 - 49: 7.223 distance: 39 - 40: 34.298 distance: 39 - 43: 17.753 distance: 39 - 44: 8.869 distance: 40 - 41: 45.507 distance: 40 - 45: 45.787 distance: 40 - 46: 31.911 distance: 41 - 47: 44.257 distance: 41 - 48: 30.313 distance: 49 - 50: 5.711 distance: 49 - 56: 14.944 distance: 50 - 51: 7.537 distance: 50 - 53: 9.068 distance: 50 - 57: 4.810 distance: 51 - 52: 10.201 distance: 51 - 63: 4.828 distance: 53 - 54: 5.739 distance: 53 - 55: 4.469 distance: 54 - 59: 7.773 distance: 55 - 60: 18.071 distance: 55 - 61: 17.525 distance: 55 - 62: 13.547 distance: 63 - 64: 4.462 distance: 63 - 71: 7.639 distance: 64 - 67: 3.756 distance: 65 - 66: 6.836 distance: 65 - 77: 3.955 distance: 70 - 75: 3.712 distance: 70 - 76: 4.423 distance: 77 - 78: 9.319 distance: 77 - 81: 4.293 distance: 78 - 79: 11.578 distance: 78 - 82: 8.567 distance: 78 - 83: 3.569 distance: 79 - 80: 26.739 distance: 79 - 84: 13.196 distance: 84 - 85: 7.930 distance: 84 - 91: 27.653 distance: 85 - 86: 4.184 distance: 85 - 88: 11.025 distance: 85 - 92: 7.448 distance: 86 - 87: 9.356 distance: 86 - 100: 8.100 distance: 88 - 89: 13.105 distance: 88 - 90: 15.097 distance: 88 - 93: 19.205 distance: 89 - 94: 7.859 distance: 89 - 95: 7.336 distance: 89 - 96: 3.187 distance: 90 - 97: 14.051 distance: 90 - 98: 18.005 distance: 90 - 99: 19.917 distance: 100 - 101: 21.488 distance: 101 - 102: 6.836 distance: 101 - 105: 22.617 distance: 101 - 106: 17.787 distance: 102 - 103: 20.376 distance: 102 - 107: 11.364 distance: 107 - 108: 5.809 distance: 107 - 119: 3.722 distance: 108 - 111: 6.790 distance: 108 - 120: 5.397 distance: 109 - 110: 12.343 distance: 109 - 128: 3.683 distance: 111 - 112: 3.663 distance: 115 - 117: 3.604 distance: 115 - 125: 4.511 distance: 116 - 117: 3.112 distance: 117 - 118: 4.458 distance: 118 - 127: 5.430 distance: 128 - 129: 5.504 distance: 128 - 137: 8.825 distance: 129 - 130: 3.452 distance: 129 - 132: 6.948 distance: 129 - 138: 4.493 distance: 132 - 133: 4.744 distance: 132 - 139: 5.878 distance: 132 - 140: 6.114