Starting phenix.real_space_refine on Mon Sep 14 06:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zdg_11173/09_2026/6zdg_11173_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zdg_11173/09_2026/6zdg_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zdg_11173/09_2026/6zdg_11173_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zdg_11173/09_2026/6zdg_11173_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zdg_11173/09_2026/6zdg_11173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zdg_11173/09_2026/6zdg_11173.map" } 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-2.2.1-6174/lib/python3.11/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: 5.26, 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: 2.64 Conformation dependent library (CDL) restraints added in 854.7 milliseconds 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: 0.69 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: 7.82 Time building geometry restraints manager: 3.68 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: 0.08 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: 17.080 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: 0.200 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.200 Find NCS groups from input model: 0.240 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 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 are 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/Z covalent geometry : bond 0.00354 / 0.17 (14907) covalent geometry : angle 0.50272 / 0.28 (20271) SS BOND : bond 0.00662 / 0.37 ( 27) SS BOND : angle 1.43620 / 1.00 ( 54) hydrogen bonds : bond 0.21732 / 14.07 ( 509) hydrogen bonds : angle 8.20242 / 5.63 ( 1419) link_NAG-ASN : bond 0.00014 / 0.01 ( 3) link_NAG-ASN : angle 1.05476 / 0.59 ( 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 : 0.088 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: 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: 0.2070 time to fit residues: 11.8524 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 : 0.100 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 : 0.107 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: 0.7651 (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: 0.1792 time to fit residues: 13.7073 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 : 0.086 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 : 0.088 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: 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: 0.1611 time to fit residues: 10.8460 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 : 0.088 ------------------------------------------------------------------------------- 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... E 394 ASN E 450 ASN ** 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: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105300 restraints weight = 10998.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.109731 restraints weight = 6202.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.112789 restraints weight = 3937.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.115013 restraints weight = 2689.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.116686 restraints weight = 1927.849| |-----------------------------------------------------------------------------| r_work (final): 0.3908 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.126997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105296 restraints weight = 13958.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.110716 restraints weight = 7404.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.114655 restraints weight = 4470.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.117573 restraints weight = 2896.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.119588 restraints weight = 1970.855| |-----------------------------------------------------------------------------| r_work (final): 0.4014 |-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: 0.6528 moved from start: 0.3258 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 : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.56 % Allowed : 1.67 % Favored : 97.78 % 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 are 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/Z covalent geometry : bond 0.02027 / 0.96 (14907) covalent geometry : angle 0.75893 / 0.49 (20271) SS BOND : bond 0.01203 / 0.72 ( 27) SS BOND : angle 1.69514 / 1.13 ( 54) hydrogen bonds : bond 0.04991 / 3.43 ( 509) hydrogen bonds : angle 6.74116 / 4.72 ( 1419) link_NAG-ASN : bond 0.00081 / 0.04 ( 3) link_NAG-ASN : angle 1.24023 / 0.74 ( 9) *********************** 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 50 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.084 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: 0.3927 (m-10) cc_final: 0.2964 (t80) REVERT: D 452 LEU cc_start: 0.8777 (mt) cc_final: 0.8514 (mt) REVERT: D 465 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7642 (tm-30) REVERT: D 514 SER cc_start: 0.8214 (p) cc_final: 0.7608 (p) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.2048 time to fit residues: 11.0580 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 : 0.082 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 : 0.090 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 outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.2006 time to fit residues: 12.0043 Evaluate side-chains 47 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.088 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 : 0.086 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 117 PHE cc_start: 0.8065 (m-80) cc_final: 0.7804 (m-80) REVERT: L 123 ASP cc_start: 0.8966 (m-30) cc_final: 0.8756 (p0) REVERT: L 214 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7190 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1329 time to fit residues: 6.0746 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 : 0.086 ------------------------------------------------------------------------------- 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: 0.9980 chunk 157 optimal weight: 0.0570 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 175 optimal weight: 0.0000 chunk 112 optimal weight: 0.0370 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.0470 overall best weight: 0.0476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN L 148 GLN D 450 ASN F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.105574 restraints weight = 10865.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.110030 restraints weight = 5982.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.113221 restraints weight = 3739.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.115433 restraints weight = 2535.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.117254 restraints weight = 1834.156| |-----------------------------------------------------------------------------| r_work (final): 0.3944 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.129055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.106191 restraints weight = 13657.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.111991 restraints weight = 7279.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116231 restraints weight = 4413.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.119361 restraints weight = 2865.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.121495 restraints weight = 1946.870| |-----------------------------------------------------------------------------| r_work (final): 0.4064 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.112529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.091595 restraints weight = 16640.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096493 restraints weight = 9560.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.100437 restraints weight = 6164.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.103049 restraints weight = 4184.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.105029 restraints weight = 3006.771| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.856 14937 Z= 0.955 Angle : 0.778 19.306 20334 Z= 0.489 Chirality : 0.047 0.256 2244 Planarity : 0.004 0.046 2601 Dihedral : 4.931 41.719 2115 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.19 % Allowed : 1.48 % Favored : 98.33 % Cbeta Deviations : 0.17 % 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 are not related in a simple way. whole: -0.01 (0.19), residues: 1860 helix: -2.38 (0.37), residues: 135 sheet: 0.60 (0.18), residues: 750 loop : -0.03 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 143 TYR 0.011 0.001 TYR D 473 PHE 0.030 0.002 PHE F 130 TRP 0.062 0.004 TRP H 104 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.02030 / 0.96 (14907) covalent geometry : angle 0.77514 / 0.49 (20271) SS BOND : bond 0.01337 / 0.73 ( 27) SS BOND : angle 1.41841 / 0.97 ( 54) hydrogen bonds : bond 0.03969 / 2.68 ( 509) hydrogen bonds : angle 6.15616 / 4.32 ( 1419) link_NAG-ASN : bond 0.00171 / 0.08 ( 3) link_NAG-ASN : angle 1.19707 / 0.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 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 45 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.084 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: D 342 PHE cc_start: 0.8357 (m-80) cc_final: 0.7611 (m-80) REVERT: D 369 TYR cc_start: 0.3675 (m-10) cc_final: 0.2826 (t80) REVERT: D 452 LEU cc_start: 0.8800 (mt) cc_final: 0.8597 (mt) REVERT: D 467 ASP cc_start: 0.7554 (t0) cc_final: 0.7057 (t0) REVERT: D 469 SER cc_start: 0.7788 (t) cc_final: 0.7403 (p) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1908 time to fit residues: 9.0254 Evaluate side-chains 32 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.081 Evaluate side-chains 55 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.092 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: F 28 THR cc_start: 0.9138 (m) cc_final: 0.8825 (m) REVERT: F 59 TYR cc_start: 0.8030 (m-80) cc_final: 0.7793 (m-10) REVERT: F 108 PHE cc_start: 0.6112 (m-10) cc_final: 0.4403 (p90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1856 time to fit residues: 11.1215 Evaluate side-chains 44 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.092 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 : 0.087 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: L 71 PHE cc_start: 0.7217 (m-80) cc_final: 0.6915 (m-80) REVERT: L 93 SER cc_start: 0.9281 (t) cc_final: 0.9034 (p) REVERT: L 191 LYS cc_start: 0.7677 (tppt) cc_final: 0.6877 (tppt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1255 time to fit residues: 5.5946 Evaluate side-chains 30 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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: 0.1980 chunk 17 optimal weight: 0.0170 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 0.0030 chunk 89 optimal weight: 0.0570 chunk 176 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 overall best weight: 0.0946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 487 ASN F 77 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 = 0.4074 r_free = 0.4074 target = 0.124584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105248 restraints weight = 13858.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.109963 restraints weight = 8275.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.113334 restraints weight = 5413.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.115658 restraints weight = 3827.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117574 restraints weight = 2884.295| |-----------------------------------------------------------------------------| r_work (final): 0.3915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.127923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106318 restraints weight = 12763.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.112186 restraints weight = 6656.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.116456 restraints weight = 3881.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.119368 restraints weight = 2431.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.121343 restraints weight = 1624.665| |-----------------------------------------------------------------------------| r_work (final): 0.4069 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.108453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.086151 restraints weight = 13714.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091089 restraints weight = 7553.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094910 restraints weight = 4744.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.097749 restraints weight = 3226.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.100121 restraints weight = 2341.500| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 14937 Z= 0.141 Angle : 0.567 9.229 20334 Z= 0.306 Chirality : 0.046 0.264 2244 Planarity : 0.006 0.093 2601 Dihedral : 5.021 40.154 2115 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -0.05 (0.19), residues: 1860 helix: -2.05 (0.40), residues: 117 sheet: 0.61 (0.18), residues: 747 loop : -0.19 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 466 TYR 0.021 0.001 TYR H 106 PHE 0.015 0.001 PHE D 490 TRP 0.052 0.003 TRP F 104 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (14907) covalent geometry : angle 0.56246 / 0.30 (20271) SS BOND : bond 0.01396 / 0.76 ( 27) SS BOND : angle 1.44639 / 0.98 ( 54) hydrogen bonds : bond 0.03655 / 2.49 ( 509) hydrogen bonds : angle 5.94237 / 4.17 ( 1419) link_NAG-ASN : bond 0.00191 / 0.09 ( 3) link_NAG-ASN : angle 1.03712 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 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 41 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.103 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: 0.3815 (m-10) cc_final: 0.2211 (t80) REVERT: E 421 TYR cc_start: 0.6863 (m-10) cc_final: 0.6429 (m-10) REVERT: E 457 ARG cc_start: 0.9090 (ttt-90) cc_final: 0.8594 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2185 time to fit residues: 9.6673 Evaluate side-chains 30 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.082 Evaluate side-chains 54 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.089 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: F 59 TYR cc_start: 0.8032 (m-80) cc_final: 0.7782 (m-10) REVERT: F 108 PHE cc_start: 0.6066 (m-10) cc_final: 0.4341 (p90) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1882 time to fit residues: 11.1208 Evaluate side-chains 44 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.086 Evaluate side-chains 35 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.089 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 93 SER cc_start: 0.8282 (t) cc_final: 0.7985 (t) REVERT: C 106 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7220 (mp0) REVERT: C 196 GLU cc_start: 0.9207 (tt0) cc_final: 0.8725 (tm-30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1134 time to fit residues: 4.6019 Evaluate side-chains 27 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 0.0980 chunk 75 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 127 optimal weight: 0.0980 chunk 143 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 487 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 = 0.4070 r_free = 0.4070 target = 0.124451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105610 restraints weight = 11604.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.109919 restraints weight = 6812.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.113167 restraints weight = 4458.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.115595 restraints weight = 3122.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.117348 restraints weight = 2303.488| |-----------------------------------------------------------------------------| r_work (final): 0.3934 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.122944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098464 restraints weight = 13179.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104175 restraints weight = 7369.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108655 restraints weight = 4685.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.111926 restraints weight = 3144.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114180 restraints weight = 2198.225| |-----------------------------------------------------------------------------| r_work (final): 0.3885 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.111748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086789 restraints weight = 14804.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091621 restraints weight = 8185.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.095410 restraints weight = 5263.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.098353 restraints weight = 3658.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.100598 restraints weight = 2700.298| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14937 Z= 0.156 Angle : 0.546 7.253 20334 Z= 0.298 Chirality : 0.044 0.181 2244 Planarity : 0.005 0.077 2601 Dihedral : 5.081 36.660 2115 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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 are not related in a simple way. whole: -0.19 (0.19), residues: 1860 helix: -1.76 (0.42), residues: 117 sheet: 0.55 (0.18), residues: 735 loop : -0.37 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.027 0.002 TYR C 32 PHE 0.013 0.002 PHE E 392 TRP 0.012 0.002 TRP H 104 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (14907) covalent geometry : angle 0.54045 / 0.30 (20271) SS BOND : bond 0.01224 / 0.66 ( 27) SS BOND : angle 1.49851 / 1.01 ( 54) hydrogen bonds : bond 0.03264 / 2.16 ( 509) hydrogen bonds : angle 5.77443 / 4.03 ( 1419) link_NAG-ASN : bond 0.00007 / 0.00 ( 3) link_NAG-ASN : angle 1.04837 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 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 39 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.081 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: E 357 ARG cc_start: 0.6434 (ttt-90) cc_final: 0.6115 (tmt170) REVERT: E 369 TYR cc_start: 0.3851 (m-10) cc_final: 0.2248 (t80) REVERT: E 452 LEU cc_start: 0.8522 (mt) cc_final: 0.8228 (mt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2489 time to fit residues: 10.3639 Evaluate side-chains 32 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.081 Evaluate side-chains 44 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 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: H 108 PHE cc_start: 0.5898 (m-10) cc_final: 0.3874 (p90) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1929 time to fit residues: 9.2740 Evaluate side-chains 39 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.089 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 : 0.091 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: C 106 GLU cc_start: 0.8689 (mm-30) cc_final: 0.7499 (mp0) REVERT: C 117 PHE cc_start: 0.7537 (m-80) cc_final: 0.7335 (m-80) REVERT: C 196 GLU cc_start: 0.9213 (tt0) cc_final: 0.8720 (tm-30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1180 time to fit residues: 4.2335 Evaluate side-chains 26 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 111 optimal weight: 0.6980 chunk 12 optimal weight: 0.0030 chunk 30 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 77 optimal weight: 0.0060 chunk 88 optimal weight: 0.0670 chunk 102 optimal weight: 0.0370 chunk 155 optimal weight: 0.1980 overall best weight: 0.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 487 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 = 0.4101 r_free = 0.4101 target = 0.126077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.107325 restraints weight = 11334.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.111548 restraints weight = 6566.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114968 restraints weight = 4278.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117423 restraints weight = 2962.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.119237 restraints weight = 2171.600| |-----------------------------------------------------------------------------| r_work (final): 0.3982 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.127646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104593 restraints weight = 12870.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.110202 restraints weight = 7122.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114488 restraints weight = 4378.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.117773 restraints weight = 2849.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.120117 restraints weight = 1918.804| |-----------------------------------------------------------------------------| r_work (final): 0.4022 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.112974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088911 restraints weight = 16488.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093780 restraints weight = 9694.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.097658 restraints weight = 6327.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.100743 restraints weight = 4482.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.103045 restraints weight = 3318.676| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14937 Z= 0.103 Angle : 0.510 7.244 20334 Z= 0.274 Chirality : 0.044 0.156 2244 Planarity : 0.004 0.068 2601 Dihedral : 4.727 31.804 2115 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 are not related in a simple way. whole: -0.03 (0.19), residues: 1860 helix: -1.62 (0.43), residues: 117 sheet: 0.60 (0.18), residues: 777 loop : -0.25 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.017 0.001 TYR B 59 PHE 0.011 0.001 PHE A 490 TRP 0.015 0.002 TRP B 104 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14907) covalent geometry : angle 0.50481 / 0.27 (20271) SS BOND : bond 0.01176 / 0.65 ( 27) SS BOND : angle 1.41773 / 0.96 ( 54) hydrogen bonds : bond 0.03006 / 2.01 ( 509) hydrogen bonds : angle 5.49847 / 3.84 ( 1419) link_NAG-ASN : bond 0.00197 / 0.09 ( 3) link_NAG-ASN : angle 1.00956 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 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 40 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.084 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: E 369 TYR cc_start: 0.3834 (m-10) cc_final: 0.2359 (t80) REVERT: E 452 LEU cc_start: 0.8512 (mt) cc_final: 0.8254 (mt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2263 time to fit residues: 9.6916 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 : 0.075 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 : 0.090 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: F 108 PHE cc_start: 0.5612 (m-10) cc_final: 0.3978 (p90) REVERT: F 117 VAL cc_start: 0.8468 (t) cc_final: 0.8252 (t) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1860 time to fit residues: 9.7454 Evaluate side-chains 42 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.090 Evaluate side-chains 33 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.105 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 93 SER cc_start: 0.8489 (t) cc_final: 0.8208 (t) REVERT: C 106 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7522 (mp0) REVERT: C 196 GLU cc_start: 0.9181 (tt0) cc_final: 0.8696 (tm-30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0974 time to fit residues: 3.8026 Evaluate side-chains 27 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 108 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 140 optimal weight: 0.0970 chunk 98 optimal weight: 0.5980 chunk 96 optimal weight: 0.0030 chunk 82 optimal weight: 0.0270 chunk 13 optimal weight: 0.0670 chunk 136 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 34 optimal weight: 0.0370 overall best weight: 0.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 487 ASN F 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.128081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.109736 restraints weight = 11235.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113999 restraints weight = 6349.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.117551 restraints weight = 4097.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.120152 restraints weight = 2793.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.121922 restraints weight = 1982.342| |-----------------------------------------------------------------------------| r_work (final): 0.4019 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.129974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.107078 restraints weight = 14089.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.112566 restraints weight = 8196.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.116819 restraints weight = 5250.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.120050 restraints weight = 3512.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.122428 restraints weight = 2416.864| |-----------------------------------------------------------------------------| r_work (final): 0.4062 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.112217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.087333 restraints weight = 14616.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.092293 restraints weight = 8385.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096211 restraints weight = 5396.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099259 restraints weight = 3738.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.101661 restraints weight = 2767.211| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14937 Z= 0.095 Angle : 0.494 6.949 20334 Z= 0.263 Chirality : 0.044 0.156 2244 Planarity : 0.004 0.063 2601 Dihedral : 4.460 27.559 2115 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 are not related in a simple way. whole: 0.04 (0.19), residues: 1860 helix: -1.48 (0.44), residues: 117 sheet: 0.77 (0.18), residues: 744 loop : -0.30 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 466 TYR 0.026 0.001 TYR B 106 PHE 0.020 0.001 PHE D 392 TRP 0.008 0.001 TRP H 162 HIS 0.004 0.001 HIS F 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (14907) covalent geometry : angle 0.48896 / 0.26 (20271) SS BOND : bond 0.01287 / 0.74 ( 27) SS BOND : angle 1.41265 / 0.98 ( 54) hydrogen bonds : bond 0.02838 / 1.92 ( 509) hydrogen bonds : angle 5.30414 / 3.69 ( 1419) link_NAG-ASN : bond 0.00211 / 0.10 ( 3) link_NAG-ASN : angle 1.09421 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 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 38 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.083 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: E 369 TYR cc_start: 0.3670 (m-10) cc_final: 0.2277 (t80) REVERT: E 452 LEU cc_start: 0.8486 (mt) cc_final: 0.8228 (mt) REVERT: E 486 PHE cc_start: 0.7810 (t80) cc_final: 0.7253 (t80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2441 time to fit residues: 9.9027 Evaluate side-chains 28 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.084 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 : 0.095 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: F 83 MET cc_start: 0.7295 (ptp) cc_final: 0.7075 (ptp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1974 time to fit residues: 10.5438 Evaluate side-chains 42 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.086 Evaluate side-chains 33 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.083 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 93 SER cc_start: 0.8591 (t) cc_final: 0.8336 (t) REVERT: C 106 GLU cc_start: 0.8586 (mm-30) cc_final: 0.7558 (mp0) REVERT: C 196 GLU cc_start: 0.9165 (tt0) cc_final: 0.8681 (tm-30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1037 time to fit residues: 4.0086 Evaluate side-chains 26 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 0.0170 chunk 123 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 481 ASN E 487 ASN F 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.122957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104621 restraints weight = 11498.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.108796 restraints weight = 6636.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111937 restraints weight = 4288.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.114325 restraints weight = 3007.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.116246 restraints weight = 2236.628| |-----------------------------------------------------------------------------| r_work (final): 0.3925 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.125601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.104278 restraints weight = 14371.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.109378 restraints weight = 8246.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.113283 restraints weight = 5210.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116091 restraints weight = 3468.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.118290 restraints weight = 2427.912| |-----------------------------------------------------------------------------| r_work (final): 0.3981 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.109219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085734 restraints weight = 15545.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.090087 restraints weight = 9239.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093595 restraints weight = 6199.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096399 restraints weight = 4462.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.098597 restraints weight = 3351.958| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5692 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= 0.181 Angle : 0.556 6.086 20334 Z= 0.300 Chirality : 0.042 0.141 2244 Planarity : 0.005 0.064 2601 Dihedral : 4.749 24.970 2115 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 are not related in a simple way. whole: -0.21 (0.19), residues: 1860 helix: -1.26 (0.46), residues: 117 sheet: 0.48 (0.18), residues: 777 loop : -0.45 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 24 TYR 0.020 0.002 TYR F 94 PHE 0.020 0.002 PHE E 400 TRP 0.020 0.002 TRP F 104 HIS 0.007 0.002 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (14907) covalent geometry : angle 0.55019 / 0.30 (20271) SS BOND : bond 0.01223 / 0.68 ( 27) SS BOND : angle 1.60127 / 1.04 ( 54) hydrogen bonds : bond 0.03100 / 2.08 ( 509) hydrogen bonds : angle 5.61960 / 3.93 ( 1419) link_NAG-ASN : bond 0.00041 / 0.02 ( 3) link_NAG-ASN : angle 1.33344 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 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 35 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.081 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 357 ARG cc_start: 0.6848 (ttt-90) cc_final: 0.6388 (tmm-80) REVERT: E 369 TYR cc_start: 0.3701 (m-10) cc_final: 0.2150 (t80) REVERT: E 452 LEU cc_start: 0.8676 (mt) cc_final: 0.8368 (mt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2509 time to fit residues: 9.3490 Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.085 Evaluate side-chains 47 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.081 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: F 83 MET cc_start: 0.7528 (ptp) cc_final: 0.7158 (ptp) REVERT: F 108 PHE cc_start: 0.5636 (m-10) cc_final: 0.3948 (p90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1720 time to fit residues: 8.8055 Evaluate side-chains 43 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.090 Evaluate side-chains 34 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.100 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 93 SER cc_start: 0.8584 (t) cc_final: 0.8350 (t) REVERT: C 196 GLU cc_start: 0.9113 (tt0) cc_final: 0.8655 (tm-30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1105 time to fit residues: 4.3945 Evaluate side-chains 25 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 487 ASN F 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.126015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107018 restraints weight = 12703.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.111663 restraints weight = 7354.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.115020 restraints weight = 4785.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117467 restraints weight = 3362.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.119264 restraints weight = 2494.550| |-----------------------------------------------------------------------------| r_work (final): 0.3968 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.126792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104154 restraints weight = 14318.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.109686 restraints weight = 8238.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.113876 restraints weight = 5175.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117091 restraints weight = 3403.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119244 restraints weight = 2322.138| |-----------------------------------------------------------------------------| r_work (final): 0.3997 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.114056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087717 restraints weight = 16707.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.093061 restraints weight = 9200.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097032 restraints weight = 5852.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.100367 restraints weight = 4112.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.102957 restraints weight = 3015.880| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14937 Z= 0.122 Angle : 0.509 6.256 20334 Z= 0.275 Chirality : 0.043 0.157 2244 Planarity : 0.004 0.061 2601 Dihedral : 4.552 22.998 2115 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 are not related in a simple way. whole: -0.20 (0.19), residues: 1860 helix: -1.37 (0.45), residues: 117 sheet: 0.50 (0.18), residues: 774 loop : -0.44 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 466 TYR 0.010 0.001 TYR B 95 PHE 0.023 0.002 PHE E 377 TRP 0.019 0.002 TRP B 104 HIS 0.003 0.001 HIS F 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14907) covalent geometry : angle 0.50163 / 0.27 (20271) SS BOND : bond 0.01236 / 0.69 ( 27) SS BOND : angle 1.73757 / 1.15 ( 54) hydrogen bonds : bond 0.02958 / 1.99 ( 509) hydrogen bonds : angle 5.60171 / 3.91 ( 1419) link_NAG-ASN : bond 0.00134 / 0.06 ( 3) link_NAG-ASN : angle 1.19970 / 0.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 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 35 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.082 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: E 369 TYR cc_start: 0.3903 (m-10) cc_final: 0.2288 (t80) REVERT: E 452 LEU cc_start: 0.8603 (mt) cc_final: 0.8335 (mt) REVERT: E 472 ILE cc_start: 0.7534 (tp) cc_final: 0.7330 (tp) REVERT: E 487 ASN cc_start: 0.6854 (m110) cc_final: 0.6614 (m-40) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2293 time to fit residues: 8.6183 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 : 0.050 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 : 0.057 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 outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1921 time to fit residues: 9.3470 Evaluate side-chains 41 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.094 Evaluate side-chains 30 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 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: C 93 SER cc_start: 0.8579 (t) cc_final: 0.8334 (t) REVERT: C 106 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7562 (mp0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0884 time to fit residues: 3.1662 Evaluate side-chains 26 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 102 optimal weight: 0.9990 chunk 148 optimal weight: 0.0980 chunk 21 optimal weight: 0.0270 chunk 17 optimal weight: 0.1980 chunk 71 optimal weight: 0.0000 chunk 143 optimal weight: 0.0060 chunk 72 optimal weight: 0.8980 overall best weight: 0.0436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.128108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.110441 restraints weight = 12280.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.114716 restraints weight = 7029.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117868 restraints weight = 4614.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.120210 restraints weight = 3280.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.121977 restraints weight = 2443.581| |-----------------------------------------------------------------------------| r_work (final): 0.4021 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.127714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.105559 restraints weight = 13923.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.111005 restraints weight = 7776.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.115308 restraints weight = 4783.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.118279 restraints weight = 3070.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.120379 restraints weight = 2079.355| |-----------------------------------------------------------------------------| r_work (final): 0.4022 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089126 restraints weight = 16070.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094347 restraints weight = 9146.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.098374 restraints weight = 5858.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.101464 restraints weight = 4086.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.103692 restraints weight = 2987.055| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14937 Z= 0.097 Angle : 0.498 6.395 20334 Z= 0.264 Chirality : 0.044 0.154 2244 Planarity : 0.004 0.057 2601 Dihedral : 4.241 20.237 2115 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 are not related in a simple way. whole: -0.04 (0.20), residues: 1860 helix: -1.35 (0.45), residues: 117 sheet: 0.63 (0.18), residues: 774 loop : -0.33 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 408 TYR 0.018 0.001 TYR H 106 PHE 0.018 0.001 PHE E 377 TRP 0.020 0.002 TRP F 104 HIS 0.003 0.001 HIS F 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (14907) covalent geometry : angle 0.48992 / 0.26 (20271) SS BOND : bond 0.01216 / 0.68 ( 27) SS BOND : angle 1.70957 / 1.10 ( 54) hydrogen bonds : bond 0.02940 / 1.97 ( 509) hydrogen bonds : angle 5.31503 / 3.70 ( 1419) link_NAG-ASN : bond 0.00245 / 0.11 ( 3) link_NAG-ASN : angle 1.20928 / 0.72 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 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 37 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.081 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: E 369 TYR cc_start: 0.3814 (m-10) cc_final: 0.2355 (t80) REVERT: E 452 LEU cc_start: 0.8488 (mt) cc_final: 0.8227 (mt) REVERT: E 472 ILE cc_start: 0.7411 (tp) cc_final: 0.7199 (tp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1682 time to fit residues: 6.7857 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 : 0.074 Evaluate side-chains 47 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.052 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: F 108 PHE cc_start: 0.5294 (m-10) cc_final: 0.3560 (p90) REVERT: F 154 PHE cc_start: 0.7884 (t80) cc_final: 0.7577 (t80) REVERT: F 184 TYR cc_start: 0.7618 (m-80) cc_final: 0.7379 (m-80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1636 time to fit residues: 8.3256 Evaluate side-chains 42 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.055 Evaluate side-chains 28 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.092 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 93 SER cc_start: 0.8662 (t) cc_final: 0.8244 (p) REVERT: C 106 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7486 (mp0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0996 time to fit residues: 3.3171 Evaluate side-chains 23 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 105 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 chunk 131 optimal weight: 0.0970 chunk 174 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 487 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 = 0.4088 r_free = 0.4088 target = 0.125240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.107320 restraints weight = 12551.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.111560 restraints weight = 7240.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114787 restraints weight = 4722.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.117154 restraints weight = 3339.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.118772 restraints weight = 2479.567| |-----------------------------------------------------------------------------| r_work (final): 0.3957 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.126944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.104672 restraints weight = 14158.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109958 restraints weight = 8073.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114028 restraints weight = 5065.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.117010 restraints weight = 3365.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.118731 restraints weight = 2347.884| |-----------------------------------------------------------------------------| r_work (final): 0.3980 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.111019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087262 restraints weight = 16589.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.092196 restraints weight = 9424.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096210 restraints weight = 6132.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099240 restraints weight = 4281.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.101310 restraints weight = 3158.452| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14937 Z= 0.112 Angle : 0.486 6.170 20334 Z= 0.260 Chirality : 0.042 0.141 2244 Planarity : 0.004 0.060 2601 Dihedral : 4.193 18.929 2115 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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 are not related in a simple way. whole: -0.13 (0.20), residues: 1860 helix: -1.13 (0.48), residues: 117 sheet: 0.55 (0.18), residues: 774 loop : -0.41 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 466 TYR 0.011 0.001 TYR F 94 PHE 0.019 0.001 PHE E 377 TRP 0.022 0.002 TRP B 104 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14907) covalent geometry : angle 0.47828 / 0.26 (20271) SS BOND : bond 0.01192 / 0.66 ( 27) SS BOND : angle 1.64487 / 1.07 ( 54) hydrogen bonds : bond 0.02853 / 1.92 ( 509) hydrogen bonds : angle 5.37689 / 3.75 ( 1419) link_NAG-ASN : bond 0.00164 / 0.08 ( 3) link_NAG-ASN : angle 1.10001 / 0.65 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2803.48 seconds wall clock time: 49 minutes 7.34 seconds (2947.34 seconds total)