Starting phenix.real_space_refine on Wed Dec 13 19:13:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/12_2023/8ddw_27344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/12_2023/8ddw_27344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/12_2023/8ddw_27344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/12_2023/8ddw_27344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/12_2023/8ddw_27344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/12_2023/8ddw_27344.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 175 5.16 5 C 16413 2.51 5 N 4530 2.21 5 O 4751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 351": "OE1" <-> "OE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25869 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 5765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5765 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 23, 'TRANS': 695} Chain breaks: 5 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 2598 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} bond proxies already assigned to first conformer: 2631 Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 14.78, per 1000 atoms: 0.57 Number of scatterers: 25869 At special positions: 0 Unit cell: (145.8, 190.08, 124.2, 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 175 16.00 O 4751 8.00 N 4530 7.00 C 16413 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 - 3.50 Amino acid : False - 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: 10.45 Conformation dependent library (CDL) restraints added in 5.4 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6134 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 14 sheets defined 55.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.674A pdb=" N LEU A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.930A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.802A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 307 through 322 removed outlier: 4.320A pdb=" N LEU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.700A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.648A pdb=" N LYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.683A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.613A pdb=" N ILE A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.744A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 4.100A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.006A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.589A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.527A pdb=" N LEU A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.789A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.700A pdb=" N MET A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 758 " --> pdb=" O CYS A 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 removed outlier: 3.568A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A1001 " --> pdb=" O GLY A 997 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A1002 " --> pdb=" O PRO A 998 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1117 removed outlier: 3.608A pdb=" N THR A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.668A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1215 Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.965A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.561A pdb=" N LEU B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 removed outlier: 4.101A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 4.002A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.622A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.730A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.966A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.607A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.598A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 removed outlier: 3.753A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.658A pdb=" N ILE B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.313A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.938A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 689 through 717 removed outlier: 4.320A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 729 through 733 removed outlier: 4.163A pdb=" N SER B 733 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 745 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 752 through 762 removed outlier: 3.752A pdb=" N LEU B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1007 Processing helix chain 'B' and resid 1110 through 1117 Processing helix chain 'B' and resid 1118 through 1142 removed outlier: 4.520A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.864A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.666A pdb=" N UNK F 5 " --> pdb=" O UNK F 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.836A pdb=" N LEU C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.738A pdb=" N VAL C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 244 removed outlier: 4.161A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 369 through 379 removed outlier: 4.106A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.230A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.752A pdb=" N LEU C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.733A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 497 removed outlier: 3.767A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.776A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 removed outlier: 4.102A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.552A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 689 through 717 Processing helix chain 'C' and resid 718 through 724 Processing helix chain 'C' and resid 729 through 733 removed outlier: 3.962A pdb=" N SER C 733 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 745 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 752 through 760 removed outlier: 4.322A pdb=" N LEU C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1007 removed outlier: 3.920A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET C1001 " --> pdb=" O GLY C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1116 Processing helix chain 'C' and resid 1118 through 1142 removed outlier: 4.535A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1215 removed outlier: 3.609A pdb=" N SER C1215 " --> pdb=" O ARG C1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.557A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.877A pdb=" N LEU D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 4.177A pdb=" N PHE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 308 through 322 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 365 through 368 removed outlier: 3.871A pdb=" N GLY D 368 " --> pdb=" O ASP D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 369 through 379 removed outlier: 4.237A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.943A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 451 removed outlier: 3.533A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 578 through 588 Processing helix chain 'D' and resid 596 through 601 removed outlier: 3.920A pdb=" N LEU D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.750A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 Processing helix chain 'D' and resid 663 through 685 removed outlier: 3.529A pdb=" N ASN D 685 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 717 removed outlier: 4.254A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 725 removed outlier: 3.873A pdb=" N LEU D 725 " --> pdb=" O ALA D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 745 Processing helix chain 'D' and resid 746 through 752 Processing helix chain 'D' and resid 752 through 761 removed outlier: 3.914A pdb=" N ASP D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1005 removed outlier: 4.008A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET D1001 " --> pdb=" O GLY D 997 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D1003 " --> pdb=" O TYR D 999 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D1005 " --> pdb=" O MET D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1117 Processing helix chain 'D' and resid 1118 through 1142 removed outlier: 4.890A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 4.000A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 26 removed outlier: 3.814A pdb=" N GLN I 9 " --> pdb=" O ASP I 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN I 17 " --> pdb=" O GLN I 13 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 removed outlier: 3.642A pdb=" N ILE I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 29 through 34' Processing helix chain 'J' and resid 9 through 24 removed outlier: 3.652A pdb=" N ARG J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 39 removed outlier: 3.638A pdb=" N ALA J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 275 removed outlier: 4.046A pdb=" N VAL A 270 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 143 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 272 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 155 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 364 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.818A pdb=" N VAL B 270 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 143 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 145 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 157 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE B 294 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET B 156 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU B 296 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 158 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP B 298 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 160 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL B 339 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS B 189 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N CYS B 364 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 338 " --> pdb=" O CYS B 364 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 361 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE B 430 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 363 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 273 through 275 removed outlier: 8.553A pdb=" N TYR C 274 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU C 145 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 155 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE C 294 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N MET C 156 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 296 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 158 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP C 298 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 160 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLY C 300 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN C 299 " --> pdb=" O TRP C 256 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL C 362 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA C 336 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N CYS C 364 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE C 338 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.793A pdb=" N SER D 136 " --> pdb=" O UNK H 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 271 through 275 removed outlier: 8.094A pdb=" N ARG D 272 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR D 143 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR D 274 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU D 145 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 157 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 155 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE D 294 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N MET D 156 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 296 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 158 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP D 298 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 160 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL D 361 " --> pdb=" O THR D 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.367A pdb=" N ILE I 338 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR I 50 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU I 336 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL I 327 " --> pdb=" O TRP I 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 58 through 63 removed outlier: 7.293A pdb=" N ALA I 73 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET I 61 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 71 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 63 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU I 69 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE I 80 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER I 74 " --> pdb=" O LYS I 78 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS I 91 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP I 83 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS I 89 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.835A pdb=" N GLY I 115 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS I 121 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU I 138 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE I 123 " --> pdb=" O SER I 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 146 through 151 removed outlier: 4.000A pdb=" N CYS I 148 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER I 161 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR I 165 " --> pdb=" O SER I 161 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU I 168 " --> pdb=" O THR I 178 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR I 178 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP I 170 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN I 176 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 187 through 192 removed outlier: 4.004A pdb=" N SER I 201 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS I 209 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA I 203 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER I 207 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA I 208 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR I 221 " --> pdb=" O ALA I 208 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU I 210 " --> pdb=" O ARG I 219 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET I 217 " --> pdb=" O ASP I 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 231 through 234 removed outlier: 3.854A pdb=" N PHE I 241 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE I 253 " --> pdb=" O PHE I 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 273 through 277 Processing sheet with id=AB5, first strand: chain 'I' and resid 294 through 295 removed outlier: 4.045A pdb=" N CYS I 294 " --> pdb=" O LEU I 308 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3641 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: 8.96 Time building geometry restraints manager: 11.12 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: 8353 1.34 - 1.45: 3435 1.45 - 1.57: 14279 1.57 - 1.69: 0 1.69 - 1.81: 297 Bond restraints: 26364 Sorted by residual: bond pdb=" CA PRO D 629 " pdb=" C PRO D 629 " ideal model delta sigma weight residual 1.526 1.492 0.034 8.50e-03 1.38e+04 1.62e+01 bond pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.29e-02 6.01e+03 1.33e+01 bond pdb=" N HIS D 633 " pdb=" CA HIS D 633 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N PHE D 634 " pdb=" CA PHE D 634 " ideal model delta sigma weight residual 1.456 1.419 0.036 1.13e-02 7.83e+03 1.04e+01 bond pdb=" CA HIS D 633 " pdb=" C HIS D 633 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.17e-02 7.31e+03 8.31e+00 ... (remaining 26359 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 608 106.26 - 113.19: 14518 113.19 - 120.13: 8817 120.13 - 127.06: 11350 127.06 - 133.99: 291 Bond angle restraints: 35584 Sorted by residual: angle pdb=" N ASN D 632 " pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 111.54 99.89 11.65 1.36e+00 5.41e-01 7.34e+01 angle pdb=" N GLU D 630 " pdb=" CA GLU D 630 " pdb=" C GLU D 630 " ideal model delta sigma weight residual 110.80 100.69 10.11 2.13e+00 2.20e-01 2.25e+01 angle pdb=" C ASN D 632 " pdb=" N HIS D 633 " pdb=" CA HIS D 633 " ideal model delta sigma weight residual 122.77 117.10 5.67 1.41e+00 5.03e-01 1.62e+01 angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 110.70 105.88 4.82 1.22e+00 6.72e-01 1.56e+01 angle pdb=" C ASP I 195 " pdb=" N THR I 196 " pdb=" CA THR I 196 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 ... (remaining 35579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 14369 17.45 - 34.89: 1084 34.89 - 52.34: 315 52.34 - 69.79: 90 69.79 - 87.23: 18 Dihedral angle restraints: 15876 sinusoidal: 6409 harmonic: 9467 Sorted by residual: dihedral pdb=" CA PRO J 55 " pdb=" C PRO J 55 " pdb=" N ALA J 56 " pdb=" CA ALA J 56 " ideal model delta harmonic sigma weight residual 180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE I 151 " pdb=" C PHE I 151 " pdb=" N LEU I 152 " pdb=" CA LEU I 152 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 15873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3378 0.054 - 0.107: 553 0.107 - 0.161: 60 0.161 - 0.214: 1 0.214 - 0.268: 1 Chirality restraints: 3993 Sorted by residual: chirality pdb=" CA HIS D 633 " pdb=" N HIS D 633 " pdb=" C HIS D 633 " pdb=" CB HIS D 633 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE D 631 " pdb=" N ILE D 631 " pdb=" C ILE D 631 " pdb=" CB ILE D 631 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE I 120 " pdb=" N ILE I 120 " pdb=" C ILE I 120 " pdb=" CB ILE I 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3990 not shown) Planarity restraints: 4551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 634 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO D 635 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 635 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 635 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 357 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 358 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 59 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO J 60 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO J 60 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 60 " -0.027 5.00e-02 4.00e+02 ... (remaining 4548 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1339 2.72 - 3.27: 27630 3.27 - 3.81: 44530 3.81 - 4.36: 51123 4.36 - 4.90: 83189 Nonbonded interactions: 207811 Sorted by model distance: nonbonded pdb=" OG SER C 556 " pdb=" OD1 ASP C 559 " model vdw 2.179 2.440 nonbonded pdb=" OH TYR I 264 " pdb=" O ALA I 299 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU C 565 " pdb=" OG1 THR C 577 " model vdw 2.187 2.440 nonbonded pdb=" O ILE A 248 " pdb=" OG SER A 292 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR C 402 " pdb=" OE1 GLN C 409 " model vdw 2.216 2.440 ... (remaining 207806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 129 through 588 or resid 632 through 1009 or resid 1109 th \ rough 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 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: 0.030 Extract box with map and model: 19.050 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 69.110 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.170 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 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 : 0.003 0.048 26364 Z= 0.179 Angle : 0.529 11.653 35584 Z= 0.298 Chirality : 0.038 0.268 3993 Planarity : 0.004 0.106 4551 Dihedral : 14.465 87.234 9742 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 8.35 % Allowed : 10.33 % Favored : 81.32 % 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: 0.15 (0.15), residues: 3148 helix: 1.52 (0.13), residues: 1602 sheet: -0.66 (0.28), residues: 359 loop : -1.67 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 483 HIS 0.008 0.001 HIS D 633 PHE 0.013 0.001 PHE B 376 TYR 0.016 0.001 TYR A 380 ARG 0.003 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 867 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 49 residues processed: 1037 average time/residue: 0.4092 time to fit residues: 646.5846 Evaluate side-chains 567 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 518 time to evaluate : 2.856 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2472 time to fit residues: 25.8437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 129 optimal weight: 50.0000 chunk 250 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 314 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 412 HIS A 490 GLN A 510 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN A 633 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A 696 ASN ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A1116 ASN B 134 GLN B 318 HIS ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 ASN C 151 HIS ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 232 HIS C 240 HIS C 279 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 378 HIS C 660 HIS C 696 ASN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C 719 GLN ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 ASN D 232 HIS D 299 ASN D 535 ASN D 548 ASN ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN I 44 GLN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26364 Z= 0.284 Angle : 0.708 9.349 35584 Z= 0.373 Chirality : 0.044 0.223 3993 Planarity : 0.005 0.087 4551 Dihedral : 4.977 27.321 3504 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 0.32 % Allowed : 5.92 % Favored : 93.76 % 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: -0.15 (0.15), residues: 3148 helix: 1.09 (0.13), residues: 1668 sheet: -0.51 (0.28), residues: 357 loop : -1.78 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 219 HIS 0.013 0.002 HIS D 639 PHE 0.044 0.003 PHE B 376 TYR 0.020 0.002 TYR C 479 ARG 0.024 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 625 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 630 average time/residue: 0.4112 time to fit residues: 403.9497 Evaluate side-chains 437 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 3.354 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2379 time to fit residues: 5.4567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 241 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 291 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS A 531 HIS A 639 HIS A 697 HIS A 719 GLN A1115 ASN A1199 GLN B 198 GLN B 314 GLN B 659 GLN B 697 HIS ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS C 151 HIS ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 232 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS C 322 GLN C 453 ASN C 475 GLN C 539 HIS C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN C 746 HIS C1199 GLN D 153 ASN D 716 GLN D 734 ASN D 739 GLN D1199 GLN I 110 ASN I 225 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26364 Z= 0.226 Angle : 0.634 11.234 35584 Z= 0.332 Chirality : 0.041 0.185 3993 Planarity : 0.004 0.054 4551 Dihedral : 4.716 26.434 3504 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 0.29 % Allowed : 4.88 % Favored : 94.84 % 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: -0.10 (0.15), residues: 3148 helix: 1.06 (0.13), residues: 1680 sheet: -0.44 (0.29), residues: 342 loop : -1.69 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D1129 HIS 0.014 0.001 HIS D 639 PHE 0.022 0.002 PHE A 162 TYR 0.016 0.002 TYR I 105 ARG 0.009 0.001 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 581 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 587 average time/residue: 0.3791 time to fit residues: 351.6611 Evaluate side-chains 420 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 418 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2623 time to fit residues: 5.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN A 719 GLN A1194 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 178 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1213 ASN D 153 ASN D 178 GLN D 293 HIS ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 734 ASN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.8310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 26364 Z= 0.313 Angle : 0.758 11.748 35584 Z= 0.399 Chirality : 0.045 0.249 3993 Planarity : 0.006 0.055 4551 Dihedral : 5.141 29.859 3504 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.20 % Favored : 93.74 % Rotamer: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.30 % 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: -0.49 (0.15), residues: 3148 helix: 0.69 (0.13), residues: 1678 sheet: -0.62 (0.29), residues: 329 loop : -1.74 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 466 HIS 0.013 0.002 HIS B 746 PHE 0.033 0.003 PHE C 517 TYR 0.029 0.002 TYR I 111 ARG 0.012 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 525 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 529 average time/residue: 0.3919 time to fit residues: 324.2452 Evaluate side-chains 380 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2724 time to fit residues: 4.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 230 optimal weight: 0.0570 chunk 127 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 ASN C 132 HIS C 151 HIS ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 515 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN C 746 HIS C1229 ASN D 240 HIS ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS D1115 ASN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.8958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26364 Z= 0.203 Angle : 0.624 10.409 35584 Z= 0.325 Chirality : 0.041 0.182 3993 Planarity : 0.004 0.054 4551 Dihedral : 4.731 27.454 3504 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % 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: -0.07 (0.15), residues: 3148 helix: 1.13 (0.13), residues: 1677 sheet: -0.36 (0.30), residues: 319 loop : -1.73 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 658 HIS 0.012 0.001 HIS D 240 PHE 0.021 0.002 PHE I 278 TYR 0.023 0.002 TYR I 289 ARG 0.011 0.001 ARG C 747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 524 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.3695 time to fit residues: 308.0309 Evaluate side-chains 381 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A1194 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN C 481 GLN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN D1115 ASN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.9927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26364 Z= 0.259 Angle : 0.671 8.820 35584 Z= 0.351 Chirality : 0.043 0.235 3993 Planarity : 0.004 0.056 4551 Dihedral : 4.806 26.925 3504 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.20 % 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: -0.12 (0.15), residues: 3148 helix: 1.09 (0.13), residues: 1688 sheet: -0.28 (0.30), residues: 311 loop : -1.81 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 658 HIS 0.009 0.001 HIS I 142 PHE 0.022 0.002 PHE I 278 TYR 0.021 0.002 TYR I 289 ARG 0.011 0.001 ARG B1226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 521 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.3886 time to fit residues: 320.6616 Evaluate side-chains 376 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 260 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A1194 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 515 HIS ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 178 GLN C 232 HIS C 288 ASN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN D1115 ASN D1127 GLN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 1.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26364 Z= 0.244 Angle : 0.670 11.622 35584 Z= 0.346 Chirality : 0.043 0.194 3993 Planarity : 0.005 0.077 4551 Dihedral : 4.870 32.099 3504 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3148 helix: 0.99 (0.13), residues: 1673 sheet: -0.59 (0.29), residues: 317 loop : -1.73 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 644 HIS 0.013 0.001 HIS I 183 PHE 0.033 0.002 PHE A 141 TYR 0.032 0.002 TYR C 527 ARG 0.007 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 489 average time/residue: 0.3776 time to fit residues: 291.4466 Evaluate side-chains 362 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2490 time to fit residues: 4.3923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 151 HIS C 291 HIS C 330 GLN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 1.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26364 Z= 0.215 Angle : 0.654 10.150 35584 Z= 0.335 Chirality : 0.043 0.338 3993 Planarity : 0.004 0.071 4551 Dihedral : 4.725 27.399 3504 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.96 % 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: -0.09 (0.15), residues: 3148 helix: 1.15 (0.13), residues: 1676 sheet: -0.49 (0.30), residues: 301 loop : -1.75 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 658 HIS 0.011 0.001 HIS B 240 PHE 0.021 0.002 PHE I 278 TYR 0.022 0.002 TYR B 527 ARG 0.008 0.001 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3763 time to fit residues: 282.9824 Evaluate side-chains 353 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 0.9980 chunk 295 optimal weight: 0.0980 chunk 269 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 286 optimal weight: 0.0670 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 539 HIS ** A1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 ASN C 151 HIS C 291 HIS C 330 GLN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** D1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 1.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26364 Z= 0.202 Angle : 0.647 9.664 35584 Z= 0.333 Chirality : 0.042 0.264 3993 Planarity : 0.004 0.066 4551 Dihedral : 4.629 27.638 3504 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.32 % 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: -0.12 (0.15), residues: 3148 helix: 1.08 (0.13), residues: 1683 sheet: -0.51 (0.30), residues: 314 loop : -1.69 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 644 HIS 0.007 0.001 HIS I 142 PHE 0.021 0.002 PHE I 278 TYR 0.024 0.001 TYR C 527 ARG 0.005 0.001 ARG B1226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 470 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 470 average time/residue: 0.3798 time to fit residues: 285.1756 Evaluate side-chains 352 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 2.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8045 > 50: distance: 57 - 61: 23.963 distance: 62 - 63: 14.300 distance: 62 - 65: 47.236 distance: 63 - 64: 14.059 distance: 63 - 67: 10.359 distance: 65 - 66: 16.264 distance: 67 - 68: 10.770 distance: 68 - 69: 48.611 distance: 68 - 71: 40.072 distance: 69 - 70: 27.247 distance: 69 - 75: 18.061 distance: 71 - 72: 31.946 distance: 72 - 73: 14.931 distance: 72 - 74: 22.672 distance: 75 - 76: 24.811 distance: 75 - 81: 21.996 distance: 76 - 77: 14.813 distance: 76 - 79: 14.669 distance: 77 - 78: 8.134 distance: 77 - 82: 27.051 distance: 79 - 80: 32.870 distance: 80 - 81: 47.221 distance: 82 - 83: 31.953 distance: 83 - 84: 23.791 distance: 83 - 86: 27.646 distance: 84 - 85: 31.696 distance: 84 - 90: 24.945 distance: 86 - 87: 15.168 distance: 87 - 88: 21.062 distance: 88 - 89: 43.783 distance: 90 - 91: 35.869 distance: 91 - 92: 27.358 distance: 91 - 94: 18.321 distance: 92 - 93: 11.096 distance: 92 - 96: 12.057 distance: 96 - 97: 25.828 distance: 97 - 98: 17.997 distance: 97 - 100: 14.596 distance: 98 - 99: 19.946 distance: 98 - 105: 10.087 distance: 100 - 101: 25.704 distance: 101 - 102: 35.938 distance: 102 - 103: 8.816 distance: 103 - 104: 8.888 distance: 105 - 106: 7.715 distance: 106 - 107: 10.547 distance: 106 - 109: 27.834 distance: 107 - 108: 10.343 distance: 107 - 113: 4.142 distance: 109 - 110: 21.791 distance: 110 - 111: 10.546 distance: 110 - 112: 9.048 distance: 113 - 114: 14.563 distance: 114 - 115: 34.603 distance: 114 - 117: 20.831 distance: 115 - 116: 15.518 distance: 115 - 120: 5.249 distance: 117 - 118: 17.842 distance: 117 - 119: 20.905 distance: 120 - 121: 13.256 distance: 121 - 122: 12.145 distance: 121 - 124: 13.124 distance: 122 - 123: 11.940 distance: 122 - 127: 6.411 distance: 124 - 125: 11.853 distance: 124 - 126: 11.991 distance: 127 - 128: 9.132 distance: 128 - 129: 11.099 distance: 128 - 131: 13.562 distance: 129 - 130: 16.402 distance: 129 - 135: 5.512 distance: 131 - 132: 14.826 distance: 132 - 133: 12.169 distance: 132 - 134: 14.613