Starting phenix.real_space_refine on Sun Jun 29 08:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lz1_30021/06_2025/6lz1_30021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lz1_30021/06_2025/6lz1_30021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lz1_30021/06_2025/6lz1_30021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lz1_30021/06_2025/6lz1_30021.map" model { file = "/net/cci-nas-00/data/ceres_data/6lz1_30021/06_2025/6lz1_30021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lz1_30021/06_2025/6lz1_30021.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 Zn 4 6.06 5 S 164 5.16 5 C 22020 2.51 5 N 5808 2.21 5 O 6496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 228 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8622 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1027} 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 23.91, per 1000 atoms: 0.69 Number of scatterers: 34492 At special positions: 0 Unit cell: (138.32, 98.8, 169.52, 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) Zn 4 29.99 S 164 16.00 O 6496 8.00 N 5808 7.00 C 22020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 8.51 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 615 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B 615 " pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 615 " pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" NE2 HIS D 615 " 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8128 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 48 sheets defined 29.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR A 561 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 592 Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 653 Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU A 784 " --> pdb=" O VAL A 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 785 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL A 961 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR B 561 " --> pdb=" O ARG B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 592 Processing helix chain 'B' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 653 Proline residue: B 632 - end of helix Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU B 784 " --> pdb=" O VAL B 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 785 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 887 Processing helix chain 'B' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL B 961 " --> pdb=" O ASP B 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS C 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 372 through 391 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU C 503 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR C 561 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 592 Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 653 Proline residue: C 632 - end of helix Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU C 784 " --> pdb=" O VAL C 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 785 " --> pdb=" O PHE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 887 Processing helix chain 'C' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL C 961 " --> pdb=" O ASP C 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS D 118 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 224 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS D 276 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 353 Processing helix chain 'D' and resid 372 through 391 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR D 561 " --> pdb=" O ARG D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 592 Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 653 Proline residue: D 632 - end of helix Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU D 784 " --> pdb=" O VAL D 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU D 785 " --> pdb=" O PHE D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 887 Processing helix chain 'D' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL D 961 " --> pdb=" O ASP D 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU A 89 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 65 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 133 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 143 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE A 193 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 284 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 489 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 286 " --> pdb=" O PHE A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 283 " --> pdb=" O LYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE A 398 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP A 548 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN A 441 " --> pdb=" O TRP A 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG A 972 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 666 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 702 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG A 747 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS A 850 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG A 929 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 852 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A 915 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER A 806 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 813 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE A 896 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER A 900 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE A 864 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 989 through 993 Processing sheet with id=AB3, first strand: chain 'A' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG A1014 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A1002 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE A1012 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A1072 " --> pdb=" O CYS A1040 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU B 89 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 65 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 133 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 143 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE B 193 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 152 through 154 Processing sheet with id=AB7, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE B 325 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 326 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 287 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 284 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE B 489 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 286 " --> pdb=" O PHE B 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE B 325 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 326 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 287 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B 283 " --> pdb=" O LYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE B 398 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP B 548 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN B 441 " --> pdb=" O TRP B 548 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG B 972 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 666 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 702 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG B 747 " --> pdb=" O ASP B 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS B 850 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG B 929 " --> pdb=" O LYS B 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 852 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 915 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER B 806 " --> pdb=" O LYS B 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 813 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE B 896 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER B 900 " --> pdb=" O PHE B 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE B 864 " --> pdb=" O SER B 900 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 989 through 993 Processing sheet with id=AC6, first strand: chain 'B' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG B1014 " --> pdb=" O SER B1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B1002 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B1012 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B1072 " --> pdb=" O CYS B1040 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU C 89 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 65 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 133 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 143 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE C 193 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 152 through 154 Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 284 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE C 489 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 286 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 283 " --> pdb=" O LYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE C 398 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP C 548 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN C 441 " --> pdb=" O TRP C 548 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG C 972 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 666 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 702 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG C 747 " --> pdb=" O ASP C 742 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS C 850 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 929 " --> pdb=" O LYS C 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 852 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY C 915 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER C 806 " --> pdb=" O LYS C 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 813 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 896 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER C 900 " --> pdb=" O PHE C 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE C 864 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 989 through 993 Processing sheet with id=AD9, first strand: chain 'C' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG C1014 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C1002 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C1012 " --> pdb=" O ILE C1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C1072 " --> pdb=" O CYS C1040 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU D 89 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D 65 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 133 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN D 143 " --> pdb=" O VAL D 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE D 193 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AE4, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE D 325 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL D 326 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE D 284 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE D 489 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 286 " --> pdb=" O PHE D 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE D 325 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL D 326 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 283 " --> pdb=" O LYS D 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE D 398 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP D 548 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 441 " --> pdb=" O TRP D 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG D 972 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 666 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 702 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG D 747 " --> pdb=" O ASP D 742 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS D 850 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG D 929 " --> pdb=" O LYS D 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 852 " --> pdb=" O LEU D 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY D 915 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER D 806 " --> pdb=" O LYS D 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 813 " --> pdb=" O SER D 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER D 817 " --> pdb=" O ILE D 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE D 896 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER D 900 " --> pdb=" O PHE D 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE D 864 " --> pdb=" O SER D 900 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 989 through 993 Processing sheet with id=AF3, first strand: chain 'D' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG D1014 " --> pdb=" O SER D1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D1002 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D1012 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D1072 " --> pdb=" O CYS D1040 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 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: 22.68 Time building geometry restraints manager: 10.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11232 1.34 - 1.46: 7696 1.46 - 1.58: 16216 1.58 - 1.69: 0 1.69 - 1.81: 232 Bond restraints: 35376 Sorted by residual: bond pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU D1017 " pdb=" C GLU D1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU A1017 " pdb=" C GLU A1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU B1017 " pdb=" C GLU B1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CG LEU D 264 " pdb=" CD2 LEU D 264 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 35371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 46152 1.40 - 2.80: 1520 2.80 - 4.20: 276 4.20 - 5.60: 56 5.60 - 7.00: 16 Bond angle restraints: 48020 Sorted by residual: angle pdb=" N GLN C 425 " pdb=" CA GLN C 425 " pdb=" CB GLN C 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN B 425 " pdb=" CA GLN B 425 " pdb=" CB GLN B 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN D 425 " pdb=" CA GLN D 425 " pdb=" CB GLN D 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN A 425 " pdb=" CA GLN A 425 " pdb=" CB GLN A 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLU C1017 " pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 110.28 103.28 7.00 1.48e+00 4.57e-01 2.24e+01 ... (remaining 48015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 18284 17.05 - 34.09: 2112 34.09 - 51.14: 424 51.14 - 68.19: 112 68.19 - 85.23: 48 Dihedral angle restraints: 20980 sinusoidal: 8400 harmonic: 12580 Sorted by residual: dihedral pdb=" CA TYR B 42 " pdb=" C TYR B 42 " pdb=" N ASP B 43 " pdb=" CA ASP B 43 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR D 42 " pdb=" C TYR D 42 " pdb=" N ASP D 43 " pdb=" CA ASP D 43 " ideal model delta harmonic sigma weight residual 180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR C 42 " pdb=" C TYR C 42 " pdb=" N ASP C 43 " pdb=" CA ASP C 43 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 20977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3664 0.045 - 0.090: 1176 0.090 - 0.135: 348 0.135 - 0.180: 16 0.180 - 0.225: 8 Chirality restraints: 5212 Sorted by residual: chirality pdb=" CA THR B 903 " pdb=" N THR B 903 " pdb=" C THR B 903 " pdb=" CB THR B 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR D 903 " pdb=" N THR D 903 " pdb=" C THR D 903 " pdb=" CB THR D 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR A 903 " pdb=" N THR A 903 " pdb=" C THR A 903 " pdb=" CB THR A 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5209 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 422 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE D 422 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE D 422 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 423 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 422 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE C 422 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE C 422 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 423 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 422 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE B 422 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE B 422 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 423 " -0.013 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 724 2.66 - 3.22: 32592 3.22 - 3.78: 55422 3.78 - 4.34: 81682 4.34 - 4.90: 135842 Nonbonded interactions: 306262 Sorted by model distance: nonbonded pdb=" OD2 ASP A 402 " pdb="ZN ZN A1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP D 402 " pdb="ZN ZN D1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP B 402 " pdb="ZN ZN B1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP C 402 " pdb="ZN ZN C1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP C 292 " pdb="ZN ZN C1201 " model vdw 2.104 2.230 ... (remaining 306257 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.210 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: 0.060 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 100.920 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.009 0.642 35380 Z= 0.320 Angle : 0.615 7.001 48020 Z= 0.360 Chirality : 0.047 0.225 5212 Planarity : 0.004 0.032 6216 Dihedral : 15.467 85.234 12852 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.52 % Allowed : 17.25 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.40 (0.11), residues: 4296 helix: -1.18 (0.13), residues: 1172 sheet: -2.09 (0.15), residues: 944 loop : -3.00 (0.11), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 159 HIS 0.004 0.001 HIS B 476 PHE 0.013 0.001 PHE A 97 TYR 0.015 0.001 TYR D 627 ARG 0.003 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.12427 ( 1428) hydrogen bonds : angle 6.61706 ( 3996) metal coordination : bond 0.64232 ( 4) covalent geometry : bond 0.00512 (35376) covalent geometry : angle 0.61474 (48020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 336 time to evaluate : 3.962 Fit side-chains REVERT: A 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7312 (m-40) REVERT: A 1004 MET cc_start: 0.8340 (mmm) cc_final: 0.8113 (tpt) REVERT: B 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7310 (m-40) REVERT: B 1004 MET cc_start: 0.8343 (mmm) cc_final: 0.8117 (tpt) REVERT: C 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7311 (m-40) REVERT: C 1004 MET cc_start: 0.8346 (mmm) cc_final: 0.8117 (tpt) REVERT: D 433 ASN cc_start: 0.7604 (m110) cc_final: 0.7314 (m-40) REVERT: D 1004 MET cc_start: 0.8347 (mmm) cc_final: 0.8117 (tpt) outliers start: 96 outliers final: 72 residues processed: 408 average time/residue: 0.4658 time to fit residues: 314.2760 Evaluate side-chains 364 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 292 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 806 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 249 optimal weight: 0.3980 chunk 388 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 137 GLN A 266 ASN A 288 HIS A 369 ASN A 412 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS A 475 GLN A 651 GLN A 758 HIS A 829 ASN A 919 HIS A 921 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 37 ASN B 266 ASN B 288 HIS B 369 ASN B 412 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 HIS B 458 ASN B 475 GLN B 651 GLN B 758 HIS B 829 ASN B 919 HIS B 921 ASN ** B 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN C 37 ASN C 266 ASN C 288 HIS C 369 ASN C 412 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 HIS C 458 ASN C 475 GLN C 651 GLN C 758 HIS C 829 ASN C 919 HIS C 921 ASN ** C 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1076 ASN D 37 ASN D 137 GLN D 266 ASN D 288 HIS D 369 ASN D 412 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS D 475 GLN D 651 GLN D 758 HIS D 829 ASN D 919 HIS D 921 ASN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1076 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097427 restraints weight = 50032.513| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.91 r_work: 0.3084 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35380 Z= 0.131 Angle : 0.543 5.906 48020 Z= 0.293 Chirality : 0.044 0.137 5212 Planarity : 0.004 0.031 6216 Dihedral : 6.629 51.561 4728 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.26 % Allowed : 16.82 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.44 (0.12), residues: 4296 helix: 0.00 (0.14), residues: 1184 sheet: -1.86 (0.15), residues: 912 loop : -2.48 (0.11), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 159 HIS 0.006 0.001 HIS B 861 PHE 0.011 0.001 PHE C 856 TYR 0.019 0.001 TYR C 627 ARG 0.006 0.000 ARG D 191 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1428) hydrogen bonds : angle 5.28542 ( 3996) metal coordination : bond 0.01282 ( 4) covalent geometry : bond 0.00296 (35376) covalent geometry : angle 0.54332 (48020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 348 time to evaluate : 3.823 Fit side-chains REVERT: A 242 MET cc_start: 0.9209 (mtp) cc_final: 0.8947 (mtm) REVERT: A 308 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7898 (ptp90) REVERT: A 412 GLN cc_start: 0.8778 (tt0) cc_final: 0.8460 (tt0) REVERT: A 433 ASN cc_start: 0.8189 (m110) cc_final: 0.7530 (m-40) REVERT: A 684 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: A 718 ASP cc_start: 0.7388 (p0) cc_final: 0.7132 (t0) REVERT: B 242 MET cc_start: 0.9205 (mtp) cc_final: 0.8943 (mtm) REVERT: B 308 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7902 (ptp90) REVERT: B 412 GLN cc_start: 0.8781 (tt0) cc_final: 0.8467 (tt0) REVERT: B 433 ASN cc_start: 0.8191 (m110) cc_final: 0.7534 (m-40) REVERT: B 684 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: B 718 ASP cc_start: 0.7405 (p0) cc_final: 0.7149 (t0) REVERT: C 242 MET cc_start: 0.9227 (mtp) cc_final: 0.8970 (mtm) REVERT: C 308 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7913 (ptp90) REVERT: C 412 GLN cc_start: 0.8768 (tt0) cc_final: 0.8454 (tt0) REVERT: C 433 ASN cc_start: 0.8196 (m110) cc_final: 0.7554 (m-40) REVERT: C 634 MET cc_start: 0.8477 (mmm) cc_final: 0.8276 (mmt) REVERT: C 684 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: C 718 ASP cc_start: 0.7414 (p0) cc_final: 0.7144 (t0) REVERT: D 242 MET cc_start: 0.9222 (mtp) cc_final: 0.8961 (mtm) REVERT: D 308 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7911 (ptp90) REVERT: D 412 GLN cc_start: 0.8775 (tt0) cc_final: 0.8461 (tt0) REVERT: D 433 ASN cc_start: 0.8198 (m110) cc_final: 0.7549 (m-40) REVERT: D 684 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: D 718 ASP cc_start: 0.7420 (p0) cc_final: 0.7156 (t0) outliers start: 124 outliers final: 68 residues processed: 440 average time/residue: 0.4782 time to fit residues: 348.5357 Evaluate side-chains 388 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 312 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 70 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 361 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 426 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN A 775 GLN A 982 ASN A1001 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN B1001 HIS ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN C1001 HIS ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN D 982 ASN D1001 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093644 restraints weight = 51182.791| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.77 r_work: 0.3022 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 35380 Z= 0.323 Angle : 0.653 6.239 48020 Z= 0.349 Chirality : 0.050 0.162 5212 Planarity : 0.004 0.044 6216 Dihedral : 6.699 58.141 4660 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.39 % Allowed : 16.75 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.12), residues: 4296 helix: 0.18 (0.15), residues: 1180 sheet: -1.79 (0.15), residues: 980 loop : -2.47 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 159 HIS 0.006 0.001 HIS D 476 PHE 0.017 0.002 PHE C 767 TYR 0.025 0.002 TYR D 627 ARG 0.005 0.001 ARG B 396 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 1428) hydrogen bonds : angle 5.37636 ( 3996) metal coordination : bond 0.00436 ( 4) covalent geometry : bond 0.00772 (35376) covalent geometry : angle 0.65253 (48020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 301 time to evaluate : 4.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7965 (m-80) cc_final: 0.7587 (m-80) REVERT: A 280 LYS cc_start: 0.8261 (ptpt) cc_final: 0.8048 (tptt) REVERT: A 308 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7984 (ptp90) REVERT: A 433 ASN cc_start: 0.8225 (m110) cc_final: 0.7403 (m-40) REVERT: A 684 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: A 716 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7873 (mmtt) REVERT: A 718 ASP cc_start: 0.7380 (p0) cc_final: 0.7077 (t0) REVERT: B 192 TYR cc_start: 0.7971 (m-80) cc_final: 0.7592 (m-80) REVERT: B 280 LYS cc_start: 0.8257 (ptpt) cc_final: 0.8046 (tptt) REVERT: B 308 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7990 (ptp90) REVERT: B 433 ASN cc_start: 0.8233 (m110) cc_final: 0.7413 (m-40) REVERT: B 684 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: B 716 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7870 (mmtt) REVERT: B 718 ASP cc_start: 0.7387 (p0) cc_final: 0.7084 (t0) REVERT: C 192 TYR cc_start: 0.7950 (m-80) cc_final: 0.7569 (m-80) REVERT: C 308 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7991 (ptp90) REVERT: C 433 ASN cc_start: 0.8236 (m110) cc_final: 0.7424 (m-40) REVERT: C 634 MET cc_start: 0.8547 (mmm) cc_final: 0.8207 (mmp) REVERT: C 684 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: C 716 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7880 (mmtt) REVERT: C 718 ASP cc_start: 0.7394 (p0) cc_final: 0.7090 (t0) REVERT: D 192 TYR cc_start: 0.7948 (m-80) cc_final: 0.7566 (m-80) REVERT: D 280 LYS cc_start: 0.8253 (ptpt) cc_final: 0.8048 (tptt) REVERT: D 308 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7988 (ptp90) REVERT: D 433 ASN cc_start: 0.8221 (m110) cc_final: 0.7410 (m-40) REVERT: D 684 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: D 716 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7874 (mmtt) REVERT: D 718 ASP cc_start: 0.7407 (p0) cc_final: 0.7103 (t0) outliers start: 167 outliers final: 116 residues processed: 433 average time/residue: 0.4855 time to fit residues: 354.1512 Evaluate side-chains 420 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 296 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 295 optimal weight: 0.4980 chunk 310 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 775 GLN B 137 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS C 137 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099088 restraints weight = 50179.827| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.93 r_work: 0.3114 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35380 Z= 0.110 Angle : 0.521 7.647 48020 Z= 0.279 Chirality : 0.044 0.151 5212 Planarity : 0.003 0.031 6216 Dihedral : 6.177 57.448 4660 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.21 % Allowed : 19.53 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4296 helix: 0.65 (0.15), residues: 1188 sheet: -1.44 (0.16), residues: 880 loop : -2.32 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 159 HIS 0.004 0.001 HIS B 861 PHE 0.011 0.001 PHE A 856 TYR 0.015 0.001 TYR D 627 ARG 0.003 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 1428) hydrogen bonds : angle 4.99498 ( 3996) metal coordination : bond 0.00086 ( 4) covalent geometry : bond 0.00248 (35376) covalent geometry : angle 0.52069 (48020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 339 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7894 (m-80) cc_final: 0.7575 (m-80) REVERT: A 308 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7905 (ptp90) REVERT: A 433 ASN cc_start: 0.8208 (m110) cc_final: 0.7508 (m-40) REVERT: A 684 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: A 716 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7844 (mmtt) REVERT: B 192 TYR cc_start: 0.7907 (m-80) cc_final: 0.7582 (m-80) REVERT: B 308 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7907 (ptp90) REVERT: B 433 ASN cc_start: 0.8201 (m110) cc_final: 0.7511 (m-40) REVERT: B 684 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: B 716 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7830 (mmtt) REVERT: C 192 TYR cc_start: 0.7883 (m-80) cc_final: 0.7562 (m-80) REVERT: C 308 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7915 (ptp90) REVERT: C 433 ASN cc_start: 0.8193 (m110) cc_final: 0.7505 (m-40) REVERT: C 684 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: C 716 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7819 (mmtt) REVERT: D 192 TYR cc_start: 0.7902 (m-80) cc_final: 0.7576 (m-80) REVERT: D 308 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7909 (ptp90) REVERT: D 433 ASN cc_start: 0.8207 (m110) cc_final: 0.7503 (m-40) REVERT: D 684 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: D 716 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7840 (mmtt) outliers start: 84 outliers final: 60 residues processed: 415 average time/residue: 0.5838 time to fit residues: 406.0399 Evaluate side-chains 361 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 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: 62.4107 > 50: distance: 92 - 114: 23.140 distance: 99 - 121: 27.119 distance: 102 - 105: 13.405 distance: 105 - 106: 13.968 distance: 106 - 107: 32.327 distance: 106 - 109: 11.999 distance: 107 - 108: 18.003 distance: 107 - 114: 17.220 distance: 108 - 143: 42.036 distance: 109 - 110: 24.358 distance: 110 - 111: 33.558 distance: 111 - 112: 29.913 distance: 111 - 113: 12.789 distance: 114 - 115: 23.740 distance: 115 - 116: 16.387 distance: 115 - 118: 15.122 distance: 116 - 117: 28.294 distance: 116 - 121: 24.250 distance: 117 - 152: 18.420 distance: 118 - 119: 30.010 distance: 118 - 120: 38.182 distance: 121 - 122: 35.038 distance: 122 - 123: 23.538 distance: 122 - 125: 35.205 distance: 123 - 124: 44.438 distance: 123 - 132: 50.861 distance: 125 - 126: 10.755 distance: 126 - 127: 7.538 distance: 127 - 128: 57.961 distance: 129 - 130: 30.938 distance: 132 - 133: 25.940 distance: 133 - 134: 10.246 distance: 133 - 136: 8.920 distance: 134 - 135: 17.638 distance: 134 - 143: 30.780 distance: 135 - 167: 27.720 distance: 136 - 137: 19.662 distance: 137 - 138: 34.065 distance: 138 - 139: 23.005 distance: 140 - 141: 5.970 distance: 140 - 142: 19.703 distance: 143 - 144: 23.968 distance: 144 - 145: 31.935 distance: 144 - 147: 14.948 distance: 145 - 146: 41.704 distance: 145 - 152: 46.261 distance: 146 - 178: 34.061 distance: 147 - 148: 8.956 distance: 148 - 149: 5.636 distance: 149 - 150: 32.688 distance: 150 - 151: 16.941 distance: 152 - 153: 20.899 distance: 153 - 154: 9.913 distance: 153 - 156: 7.402 distance: 154 - 155: 3.534 distance: 154 - 160: 12.914 distance: 155 - 184: 22.557 distance: 156 - 157: 16.490 distance: 156 - 158: 9.689 distance: 157 - 159: 3.878 distance: 160 - 161: 3.521 distance: 161 - 162: 19.408 distance: 161 - 164: 11.425 distance: 162 - 163: 13.119 distance: 162 - 167: 22.678 distance: 163 - 198: 19.365 distance: 164 - 165: 28.831 distance: 164 - 166: 4.530 distance: 167 - 168: 23.205 distance: 168 - 169: 21.662 distance: 168 - 171: 23.036 distance: 169 - 170: 9.632 distance: 169 - 178: 7.019 distance: 171 - 172: 27.384 distance: 172 - 173: 21.816 distance: 173 - 174: 13.893 distance: 174 - 175: 22.727 distance: 175 - 176: 15.341 distance: 175 - 177: 23.205 distance: 178 - 179: 19.054 distance: 179 - 180: 11.663 distance: 179 - 182: 12.266 distance: 180 - 181: 7.407 distance: 180 - 184: 14.813 distance: 181 - 210: 21.571 distance: 182 - 183: 14.815 distance: 184 - 185: 12.128 distance: 185 - 186: 3.859 distance: 185 - 188: 19.370 distance: 186 - 187: 12.901 distance: 186 - 198: 12.001 distance: 187 - 218: 18.825 distance: 188 - 189: 7.935 distance: 189 - 190: 14.544 distance: 189 - 191: 6.573 distance: 190 - 192: 14.553 distance: 191 - 193: 24.519 distance: 191 - 194: 35.833 distance: 192 - 193: 30.190 distance: 193 - 195: 11.120 distance: 194 - 196: 6.588 distance: 195 - 197: 26.984 distance: 196 - 197: 49.218