Starting phenix.real_space_refine on Fri Jun 13 22:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg9_27419/06_2025/8dg9_27419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg9_27419/06_2025/8dg9_27419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dg9_27419/06_2025/8dg9_27419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg9_27419/06_2025/8dg9_27419.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg9_27419/06_2025/8dg9_27419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg9_27419/06_2025/8dg9_27419.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.368 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9762 2.51 5 N 2568 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15450 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "B" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "C" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.80, per 1000 atoms: 0.63 Number of scatterers: 15450 At special positions: 0 Unit cell: (146.097, 140.952, 125.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3036 8.00 N 2568 7.00 C 9762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.04 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.07 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " 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 A5001 " - " ASN A 500 " " NAG A5002 " - " ASN A 27 " " NAG B 601 " - " ASN B 500 " " NAG B 602 " - " ASN B 27 " " NAG C 601 " - " ASN C 500 " " NAG C 602 " - " ASN C 27 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3714 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 36 sheets defined 24.9% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.503A pdb=" N HIS A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 217 through 239 removed outlier: 4.439A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.932A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.601A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 97 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 217 through 239 removed outlier: 4.325A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.974A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.553A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'C' and resid 74 through 97 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 217 through 239 removed outlier: 4.464A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.945A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.613A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 513 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 361 removed outlier: 8.316A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 removed outlier: 8.316A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 10.733A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.445A pdb=" N ILE A 395 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 489 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.268A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.416A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.528A pdb=" N GLY L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 358 through 361 removed outlier: 8.323A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 361 removed outlier: 8.323A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.802A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.181A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.956A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.468A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AC6, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'C' and resid 358 through 361 removed outlier: 8.263A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 361 removed outlier: 8.263A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.767A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AD2, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AD3, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.719A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.901A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AD7, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.625A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.625A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 19 through 24 768 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2571 1.30 - 1.43: 3856 1.43 - 1.56: 9169 1.56 - 1.69: 1 1.69 - 1.82: 111 Bond restraints: 15708 Sorted by residual: bond pdb=" C VAL C 349 " pdb=" O VAL C 349 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.04e-02 9.25e+03 4.38e+01 bond pdb=" C PRO E 7 " pdb=" O PRO E 7 " ideal model delta sigma weight residual 1.240 1.175 0.065 1.12e-02 7.97e+03 3.37e+01 bond pdb=" C GLY C 347 " pdb=" O GLY C 347 " ideal model delta sigma weight residual 1.237 1.188 0.048 9.40e-03 1.13e+04 2.66e+01 bond pdb=" C PRO E 8 " pdb=" O PRO E 8 " ideal model delta sigma weight residual 1.238 1.178 0.060 1.24e-02 6.50e+03 2.31e+01 bond pdb=" C ALA C 346 " pdb=" N GLY C 347 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.24e-02 6.50e+03 1.07e+01 ... (remaining 15703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 20820 1.81 - 3.62: 400 3.62 - 5.43: 52 5.43 - 7.24: 5 7.24 - 9.05: 5 Bond angle restraints: 21282 Sorted by residual: angle pdb=" C ASP C 344 " pdb=" CA ASP C 344 " pdb=" CB ASP C 344 " ideal model delta sigma weight residual 109.72 118.77 -9.05 1.66e+00 3.63e-01 2.97e+01 angle pdb=" C ALA C 346 " pdb=" N GLY C 347 " pdb=" CA GLY C 347 " ideal model delta sigma weight residual 122.83 114.60 8.23 1.80e+00 3.09e-01 2.09e+01 angle pdb=" C ASP E 50 " pdb=" N ASN E 51 " pdb=" CA ASN E 51 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N ILE C 432 " pdb=" CA ILE C 432 " pdb=" C ILE C 432 " ideal model delta sigma weight residual 112.96 109.26 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" N VAL E 11 " pdb=" CA VAL E 11 " pdb=" C VAL E 11 " ideal model delta sigma weight residual 108.45 103.04 5.41 1.48e+00 4.57e-01 1.33e+01 ... (remaining 21277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 8578 21.44 - 42.88: 824 42.88 - 64.32: 151 64.32 - 85.75: 34 85.75 - 107.19: 10 Dihedral angle restraints: 9597 sinusoidal: 3813 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS B 37 " pdb=" SG CYS B 37 " pdb=" SG CYS B 439 " pdb=" CB CYS B 439 " ideal model delta sinusoidal sigma weight residual 93.00 145.99 -52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CA ASN A 27 " pdb=" C ASN A 27 " pdb=" N ILE A 28 " pdb=" CA ILE A 28 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ARG D 98 " pdb=" C ARG D 98 " pdb=" N GLU D 99 " pdb=" CA GLU D 99 " ideal model delta harmonic sigma weight residual 180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 9594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2501 0.149 - 0.298: 5 0.298 - 0.447: 1 0.447 - 0.596: 0 0.596 - 0.745: 1 Chirality restraints: 2508 Sorted by residual: chirality pdb=" C1 NAG A5001 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG A5001 " pdb=" O5 NAG A5001 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 500 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 500 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2505 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO L 8 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E 9 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER E 9 " 0.042 2.00e-02 2.50e+03 pdb=" O SER E 9 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL E 11 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 344 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ASP C 344 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP C 344 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN C 345 " -0.014 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 223 2.67 - 3.23: 13860 3.23 - 3.79: 24569 3.79 - 4.34: 35667 4.34 - 4.90: 56600 Nonbonded interactions: 130919 Sorted by model distance: nonbonded pdb=" N GLN B 26 " pdb=" OD1 ASN B 363 " model vdw 2.116 3.120 nonbonded pdb=" OE2 GLU C 30 " pdb=" OG1 THR C 408 " model vdw 2.211 3.040 nonbonded pdb=" O PRO E 7 " pdb=" OG1 THR E 102 " model vdw 2.253 3.040 nonbonded pdb=" N GLN A 26 " pdb=" O GLY A 43 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG F 66 " pdb=" OD2 ASP F 86 " model vdw 2.266 3.120 ... (remaining 130914 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.240 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 0.093 15738 Z= 0.205 Angle : 0.666 19.956 21348 Z= 0.357 Chirality : 0.048 0.745 2508 Planarity : 0.005 0.104 2685 Dihedral : 17.358 107.193 5811 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.91 % Allowed : 23.76 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 1971 helix: 0.60 (0.25), residues: 432 sheet: 0.27 (0.21), residues: 594 loop : -0.61 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 96 HIS 0.003 0.001 HIS C 317 PHE 0.017 0.002 PHE H 67 TYR 0.019 0.002 TYR A 457 ARG 0.004 0.001 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.01523 ( 6) link_NAG-ASN : angle 6.78604 ( 18) hydrogen bonds : bond 0.19648 ( 728) hydrogen bonds : angle 7.69496 ( 1917) SS BOND : bond 0.00846 ( 24) SS BOND : angle 1.26597 ( 48) covalent geometry : bond 0.00381 (15708) covalent geometry : angle 0.63454 (21282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7583 (ttp-170) REVERT: B 176 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7880 (tttp) REVERT: B 295 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6829 (mp0) REVERT: G 5 THR cc_start: 0.8872 (m) cc_final: 0.8647 (m) REVERT: G 67 SER cc_start: 0.8059 (p) cc_final: 0.7798 (t) REVERT: C 217 ILE cc_start: 0.8422 (tp) cc_final: 0.8175 (tp) REVERT: D 43 LYS cc_start: 0.7796 (mptt) cc_final: 0.6963 (pptt) outliers start: 16 outliers final: 12 residues processed: 253 average time/residue: 1.3864 time to fit residues: 387.2244 Evaluate side-chains 228 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 115 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 426 ASN L 27BASN F 76 ASN F 81 GLN C 81 GLN C 197 ASN C 428 ASN D 76 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121227 restraints weight = 13581.452| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.23 r_work: 0.3226 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15738 Z= 0.126 Angle : 0.603 18.373 21348 Z= 0.309 Chirality : 0.046 0.599 2508 Planarity : 0.004 0.063 2685 Dihedral : 6.174 54.672 2265 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.91 % Allowed : 20.68 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 1971 helix: 1.95 (0.25), residues: 414 sheet: 0.17 (0.20), residues: 597 loop : -0.50 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 103 HIS 0.003 0.001 HIS C 317 PHE 0.013 0.002 PHE C 190 TYR 0.018 0.002 TYR B 457 ARG 0.003 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.01055 ( 6) link_NAG-ASN : angle 6.22158 ( 18) hydrogen bonds : bond 0.04201 ( 728) hydrogen bonds : angle 5.50073 ( 1917) SS BOND : bond 0.00321 ( 24) SS BOND : angle 0.69550 ( 48) covalent geometry : bond 0.00274 (15708) covalent geometry : angle 0.57503 (21282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7478 (ttp80) REVERT: L 27 ASN cc_start: 0.8022 (m-40) cc_final: 0.7495 (p0) REVERT: B 176 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8192 (tttm) REVERT: B 295 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7147 (mp0) REVERT: B 489 ASP cc_start: 0.8100 (t0) cc_final: 0.7870 (t0) REVERT: G 38 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: G 67 SER cc_start: 0.7958 (p) cc_final: 0.7611 (t) REVERT: C 489 ASP cc_start: 0.8147 (t0) cc_final: 0.7893 (t0) REVERT: D 76 ASN cc_start: 0.8364 (m-40) cc_final: 0.8156 (m-40) outliers start: 51 outliers final: 22 residues processed: 268 average time/residue: 1.2914 time to fit residues: 383.4120 Evaluate side-chains 235 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 76 ASN F 81 GLN C 197 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118285 restraints weight = 13548.891| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.22 r_work: 0.3193 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15738 Z= 0.155 Angle : 0.623 17.832 21348 Z= 0.323 Chirality : 0.047 0.574 2508 Planarity : 0.004 0.051 2685 Dihedral : 5.399 53.928 2258 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.02 % Allowed : 20.00 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 1971 helix: 2.10 (0.25), residues: 414 sheet: 0.19 (0.21), residues: 567 loop : -0.60 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 103 HIS 0.004 0.001 HIS C 317 PHE 0.013 0.002 PHE F 29 TYR 0.020 0.002 TYR B 457 ARG 0.003 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.01062 ( 6) link_NAG-ASN : angle 5.64607 ( 18) hydrogen bonds : bond 0.04400 ( 728) hydrogen bonds : angle 5.44441 ( 1917) SS BOND : bond 0.00432 ( 24) SS BOND : angle 0.69126 ( 48) covalent geometry : bond 0.00342 (15708) covalent geometry : angle 0.60127 (21282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8540 (tttp) cc_final: 0.8087 (ttmt) REVERT: H 107 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8166 (tt) REVERT: L 27 ASN cc_start: 0.8158 (m-40) cc_final: 0.7624 (p0) REVERT: B 176 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8154 (tttm) REVERT: B 295 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7090 (mp0) REVERT: G 50 ASP cc_start: 0.8607 (m-30) cc_final: 0.8405 (m-30) REVERT: C 432 ILE cc_start: 0.8738 (pt) cc_final: 0.8465 (pp) REVERT: C 489 ASP cc_start: 0.8038 (t0) cc_final: 0.7794 (t0) outliers start: 53 outliers final: 33 residues processed: 248 average time/residue: 1.2455 time to fit residues: 342.0814 Evaluate side-chains 249 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5085 > 50: distance: 19 - 292: 34.310 distance: 22 - 289: 31.933 distance: 31 - 276: 32.597 distance: 34 - 273: 19.496 distance: 43 - 257: 34.659 distance: 46 - 254: 33.566 distance: 58 - 244: 34.922 distance: 61 - 241: 36.064 distance: 170 - 283: 36.166 distance: 173 - 280: 32.839 distance: 184 - 269: 33.878 distance: 187 - 266: 26.148 distance: 198 - 252: 35.527 distance: 221 - 225: 27.453 distance: 225 - 226: 18.461 distance: 226 - 227: 41.290 distance: 226 - 229: 39.932 distance: 227 - 228: 48.448 distance: 227 - 234: 39.616 distance: 229 - 230: 7.901 distance: 230 - 231: 34.613 distance: 231 - 232: 18.086 distance: 231 - 233: 58.407 distance: 235 - 236: 10.800 distance: 235 - 238: 52.315 distance: 236 - 237: 49.501 distance: 236 - 241: 41.382 distance: 238 - 239: 52.572 distance: 238 - 240: 33.041 distance: 241 - 242: 17.788 distance: 242 - 243: 21.714 distance: 242 - 245: 44.992 distance: 243 - 249: 39.252 distance: 245 - 246: 4.409 distance: 246 - 247: 54.776 distance: 246 - 248: 40.532 distance: 249 - 250: 5.906 distance: 250 - 253: 56.704 distance: 251 - 252: 39.099 distance: 251 - 254: 69.693 distance: 254 - 255: 58.868 distance: 255 - 256: 45.184 distance: 255 - 258: 44.225 distance: 256 - 257: 56.242 distance: 256 - 266: 27.503 distance: 258 - 259: 5.540 distance: 259 - 260: 7.869 distance: 259 - 261: 33.876 distance: 260 - 262: 40.498 distance: 261 - 263: 28.069 distance: 262 - 264: 23.393 distance: 263 - 264: 7.376 distance: 264 - 265: 18.183 distance: 266 - 267: 41.937 distance: 267 - 268: 51.647 distance: 267 - 270: 43.426 distance: 268 - 269: 54.676 distance: 268 - 273: 43.655 distance: 270 - 271: 47.176 distance: 270 - 272: 46.350 distance: 273 - 274: 15.681 distance: 274 - 275: 44.160 distance: 274 - 277: 19.212 distance: 275 - 276: 39.815 distance: 275 - 280: 69.674 distance: 277 - 278: 68.952 distance: 277 - 279: 68.854 distance: 281 - 282: 55.111 distance: 281 - 284: 40.728 distance: 282 - 283: 40.047 distance: 284 - 285: 38.588 distance: 285 - 286: 14.829 distance: 286 - 287: 27.130 distance: 286 - 288: 33.743 distance: 290 - 291: 39.662 distance: 290 - 293: 55.644 distance: 291 - 292: 56.618 distance: 291 - 297: 48.090 distance: 293 - 294: 50.326 distance: 294 - 295: 56.552 distance: 294 - 296: 10.279 distance: 297 - 298: 42.399 distance: 297 - 303: 43.565 distance: 298 - 299: 38.887 distance: 298 - 301: 40.843 distance: 299 - 300: 33.235 distance: 299 - 304: 32.335 distance: 301 - 302: 5.100 distance: 302 - 303: 41.080