Starting phenix.real_space_refine on Mon Nov 20 14:12:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/11_2023/6z16_11027_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/11_2023/6z16_11027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/11_2023/6z16_11027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/11_2023/6z16_11027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/11_2023/6z16_11027_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z16_11027/11_2023/6z16_11027_updated.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 26 5.49 5 S 142 5.16 5 C 20386 2.51 5 N 4594 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 183": "NH1" <-> "NH2" Residue "a ARG 187": "NH1" <-> "NH2" Residue "a PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 473": "NH1" <-> "NH2" Residue "a ARG 644": "NH1" <-> "NH2" Residue "a ARG 789": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "d ARG 258": "NH1" <-> "NH2" Residue "f ARG 20": "NH1" <-> "NH2" Residue "g ARG 103": "NH1" <-> "NH2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 30250 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6221 Classifications: {'peptide': 788} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 758} Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3796 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 470} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 648 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "a" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6221 Classifications: {'peptide': 788} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 758} Chain: "b" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "c" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "d" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3796 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 470} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "f" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 648 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "g" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 276 Unusual residues: {' K': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "a" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 276 Unusual residues: {' K': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 16.30, per 1000 atoms: 0.54 Number of scatterers: 30250 At special positions: 0 Unit cell: (221.76, 225.12, 95.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 142 16.00 P 26 15.00 O 5098 8.00 N 4594 7.00 C 20386 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: 12.96 Conformation dependent library (CDL) restraints added in 6.0 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 8 sheets defined 70.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.38 Creating SS restraints... Processing helix chain 'A' and resid 32 through 35 No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 37 through 51 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 57 through 73 Proline residue: A 63 - end of helix removed outlier: 3.946A pdb=" N ILE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 105 through 128 Processing helix chain 'A' and resid 136 through 154 Processing helix chain 'A' and resid 159 through 177 Processing helix chain 'A' and resid 184 through 214 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 266 through 274 Processing helix chain 'A' and resid 280 through 292 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 296 through 318 removed outlier: 4.693A pdb=" N SER A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 349 removed outlier: 4.419A pdb=" N PHE A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 359 through 391 Processing helix chain 'A' and resid 407 through 421 Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.629A pdb=" N SER A 431 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 433 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 434 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 440 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 473 Proline residue: A 453 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 4.857A pdb=" N ALA A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 514 through 528 removed outlier: 5.170A pdb=" N ALA A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.817A pdb=" N MET A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 613 through 634 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 672 through 692 Processing helix chain 'A' and resid 696 through 717 Processing helix chain 'A' and resid 734 through 755 Processing helix chain 'A' and resid 765 through 769 Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 793 through 812 Processing helix chain 'B' and resid 6 through 28 Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 68 through 88 Processing helix chain 'B' and resid 114 through 137 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.986A pdb=" N CYS C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'D' and resid 2 through 19 removed outlier: 4.214A pdb=" N LEU D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Proline residue: D 8 - end of helix removed outlier: 4.960A pdb=" N ILE D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Proline residue: D 12 - end of helix Processing helix chain 'D' and resid 26 through 53 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 129 through 148 Processing helix chain 'D' and resid 153 through 183 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 238 through 262 removed outlier: 5.388A pdb=" N THR D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 296 through 315 Processing helix chain 'D' and resid 320 through 351 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 387 through 401 removed outlier: 4.209A pdb=" N ILE D 390 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY D 391 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 392 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP D 401 " --> pdb=" O ALA D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 429 Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 463 through 477 Proline residue: D 468 - end of helix Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 51 through 79 Processing helix chain 'E' and resid 100 through 111 Processing helix chain 'E' and resid 141 through 156 Processing helix chain 'F' and resid 3 through 22 Processing helix chain 'F' and resid 27 through 52 Processing helix chain 'F' and resid 58 through 79 Processing helix chain 'G' and resid 11 through 33 Processing helix chain 'G' and resid 37 through 66 Processing helix chain 'G' and resid 72 through 98 Proline residue: G 86 - end of helix Processing helix chain 'a' and resid 32 through 35 No H-bonds generated for 'chain 'a' and resid 32 through 35' Processing helix chain 'a' and resid 37 through 51 Proline residue: a 46 - end of helix Processing helix chain 'a' and resid 57 through 73 Proline residue: a 63 - end of helix removed outlier: 3.942A pdb=" N ILE a 66 " --> pdb=" O PHE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 80 Processing helix chain 'a' and resid 105 through 128 Processing helix chain 'a' and resid 136 through 155 Processing helix chain 'a' and resid 159 through 177 Processing helix chain 'a' and resid 184 through 214 Processing helix chain 'a' and resid 220 through 223 No H-bonds generated for 'chain 'a' and resid 220 through 223' Processing helix chain 'a' and resid 234 through 248 Processing helix chain 'a' and resid 255 through 257 No H-bonds generated for 'chain 'a' and resid 255 through 257' Processing helix chain 'a' and resid 261 through 263 No H-bonds generated for 'chain 'a' and resid 261 through 263' Processing helix chain 'a' and resid 266 through 275 Processing helix chain 'a' and resid 280 through 294 Proline residue: a 290 - end of helix removed outlier: 5.981A pdb=" N VAL a 294 " --> pdb=" O PRO a 290 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 318 removed outlier: 4.667A pdb=" N SER a 318 " --> pdb=" O SER a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 323 through 349 removed outlier: 4.400A pdb=" N PHE a 349 " --> pdb=" O GLY a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 353 through 355 No H-bonds generated for 'chain 'a' and resid 353 through 355' Processing helix chain 'a' and resid 359 through 391 removed outlier: 3.852A pdb=" N VAL a 363 " --> pdb=" O PHE a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 421 Processing helix chain 'a' and resid 427 through 440 removed outlier: 3.654A pdb=" N SER a 431 " --> pdb=" O GLY a 428 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET a 434 " --> pdb=" O SER a 431 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE a 436 " --> pdb=" O GLU a 433 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU a 440 " --> pdb=" O THR a 437 " (cutoff:3.500A) Processing helix chain 'a' and resid 448 through 473 Proline residue: a 453 - end of helix Processing helix chain 'a' and resid 493 through 511 removed outlier: 4.875A pdb=" N ALA a 498 " --> pdb=" O GLY a 494 " (cutoff:3.500A) Proline residue: a 499 - end of helix Processing helix chain 'a' and resid 514 through 528 removed outlier: 5.207A pdb=" N ALA a 522 " --> pdb=" O ASP a 518 " (cutoff:3.500A) Proline residue: a 523 - end of helix Processing helix chain 'a' and resid 537 through 543 Processing helix chain 'a' and resid 552 through 567 Processing helix chain 'a' and resid 574 through 583 Processing helix chain 'a' and resid 587 through 608 Processing helix chain 'a' and resid 613 through 634 Processing helix chain 'a' and resid 650 through 667 Processing helix chain 'a' and resid 672 through 692 Processing helix chain 'a' and resid 696 through 717 Processing helix chain 'a' and resid 734 through 755 Processing helix chain 'a' and resid 765 through 769 Processing helix chain 'a' and resid 781 through 786 Processing helix chain 'a' and resid 793 through 812 Processing helix chain 'b' and resid 6 through 28 Proline residue: b 17 - end of helix Processing helix chain 'b' and resid 37 through 54 Processing helix chain 'b' and resid 58 through 63 Processing helix chain 'b' and resid 68 through 88 Processing helix chain 'b' and resid 114 through 137 Processing helix chain 'c' and resid 2 through 20 Processing helix chain 'c' and resid 25 through 47 Processing helix chain 'c' and resid 67 through 97 Processing helix chain 'd' and resid 2 through 19 removed outlier: 4.209A pdb=" N LEU d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Proline residue: d 8 - end of helix removed outlier: 5.027A pdb=" N ILE d 11 " --> pdb=" O PRO d 8 " (cutoff:3.500A) Proline residue: d 12 - end of helix Processing helix chain 'd' and resid 26 through 53 Processing helix chain 'd' and resid 76 through 99 Processing helix chain 'd' and resid 102 through 106 Processing helix chain 'd' and resid 109 through 124 Processing helix chain 'd' and resid 129 through 148 Processing helix chain 'd' and resid 153 through 183 Processing helix chain 'd' and resid 189 through 198 Processing helix chain 'd' and resid 203 through 219 Processing helix chain 'd' and resid 229 through 235 Processing helix chain 'd' and resid 238 through 262 removed outlier: 5.409A pdb=" N THR d 249 " --> pdb=" O GLY d 245 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS d 250 " --> pdb=" O GLY d 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL d 251 " --> pdb=" O LEU d 247 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY d 252 " --> pdb=" O LEU d 248 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL d 253 " --> pdb=" O THR d 249 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 292 Processing helix chain 'd' and resid 296 through 315 Processing helix chain 'd' and resid 320 through 351 Processing helix chain 'd' and resid 356 through 358 No H-bonds generated for 'chain 'd' and resid 356 through 358' Processing helix chain 'd' and resid 367 through 381 Processing helix chain 'd' and resid 387 through 401 removed outlier: 4.217A pdb=" N ILE d 390 " --> pdb=" O SER d 387 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY d 391 " --> pdb=" O GLY d 388 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS d 392 " --> pdb=" O PHE d 389 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU d 393 " --> pdb=" O ILE d 390 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP d 401 " --> pdb=" O ALA d 398 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 429 Processing helix chain 'd' and resid 446 through 461 Processing helix chain 'd' and resid 463 through 477 Proline residue: d 468 - end of helix Processing helix chain 'd' and resid 481 through 487 Processing helix chain 'e' and resid 3 through 18 Processing helix chain 'e' and resid 24 through 40 Processing helix chain 'e' and resid 51 through 79 Processing helix chain 'e' and resid 100 through 111 Processing helix chain 'e' and resid 141 through 156 Processing helix chain 'f' and resid 3 through 22 Processing helix chain 'f' and resid 27 through 51 Processing helix chain 'f' and resid 58 through 79 Processing helix chain 'g' and resid 11 through 33 Processing helix chain 'g' and resid 37 through 66 Processing helix chain 'g' and resid 72 through 98 Proline residue: g 86 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 85 through 92 removed outlier: 6.969A pdb=" N ILE A 97 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 Processing sheet with id= E, first strand: chain 'a' and resid 85 through 92 removed outlier: 7.014A pdb=" N ILE a 97 " --> pdb=" O TRP a 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'd' and resid 57 through 60 Processing sheet with id= H, first strand: chain 'e' and resid 89 through 94 2003 hydrogen bonds defined for protein. 5649 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: 10.35 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4572 1.32 - 1.45: 8315 1.45 - 1.57: 17759 1.57 - 1.69: 46 1.69 - 1.82: 270 Bond restraints: 30962 Sorted by residual: bond pdb=" O14 PTY B 201 " pdb=" P1 PTY B 201 " ideal model delta sigma weight residual 1.646 1.462 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" O14 PTY E 201 " pdb=" P1 PTY E 201 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" O14 PTY a 906 " pdb=" P1 PTY a 906 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" O14 PTY A 906 " pdb=" P1 PTY A 906 " ideal model delta sigma weight residual 1.646 1.470 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" O14 PTY a 902 " pdb=" P1 PTY a 902 " ideal model delta sigma weight residual 1.646 1.470 0.176 2.00e-02 2.50e+03 7.73e+01 ... (remaining 30957 not shown) Histogram of bond angle deviations from ideal: 96.73 - 105.11: 547 105.11 - 113.49: 17619 113.49 - 121.87: 18386 121.87 - 130.25: 5195 130.25 - 138.63: 195 Bond angle restraints: 41942 Sorted by residual: angle pdb=" N PRO D 384 " pdb=" CA PRO D 384 " pdb=" C PRO D 384 " ideal model delta sigma weight residual 110.70 117.69 -6.99 1.22e+00 6.72e-01 3.28e+01 angle pdb=" N PRO d 384 " pdb=" CA PRO d 384 " pdb=" C PRO d 384 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" C ASN a 81 " pdb=" N ASP a 82 " pdb=" CA ASP a 82 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C VAL G 108 " pdb=" N ARG G 109 " pdb=" CA ARG G 109 " ideal model delta sigma weight residual 121.31 128.61 -7.30 1.49e+00 4.50e-01 2.40e+01 angle pdb=" N ALA D 235 " pdb=" CA ALA D 235 " pdb=" C ALA D 235 " ideal model delta sigma weight residual 112.17 118.78 -6.61 1.36e+00 5.41e-01 2.36e+01 ... (remaining 41937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 17721 34.92 - 69.84: 156 69.84 - 104.77: 32 104.77 - 139.69: 10 139.69 - 174.61: 5 Dihedral angle restraints: 17924 sinusoidal: 7084 harmonic: 10840 Sorted by residual: dihedral pdb=" CA ASP E 120 " pdb=" C ASP E 120 " pdb=" N VAL E 121 " pdb=" CA VAL E 121 " ideal model delta harmonic sigma weight residual 180.00 148.77 31.23 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ASP e 120 " pdb=" C ASP e 120 " pdb=" N VAL e 121 " pdb=" CA VAL e 121 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE e 49 " pdb=" C PHE e 49 " pdb=" N TYR e 50 " pdb=" CA TYR e 50 " ideal model delta harmonic sigma weight residual -180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 17921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4100 0.074 - 0.147: 762 0.147 - 0.221: 108 0.221 - 0.295: 10 0.295 - 0.369: 8 Chirality restraints: 4988 Sorted by residual: chirality pdb=" C6 PTY A 906 " pdb=" C1 PTY A 906 " pdb=" C5 PTY A 906 " pdb=" O7 PTY A 906 " both_signs ideal model delta sigma weight residual False 2.49 2.12 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C6 PTY B 201 " pdb=" C1 PTY B 201 " pdb=" C5 PTY B 201 " pdb=" O7 PTY B 201 " both_signs ideal model delta sigma weight residual False 2.49 2.13 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C6 PTY a 907 " pdb=" C1 PTY a 907 " pdb=" C5 PTY a 907 " pdb=" O7 PTY a 907 " both_signs ideal model delta sigma weight residual False 2.49 2.13 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4985 not shown) Planarity restraints: 4948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 374 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C ALA A 374 " -0.088 2.00e-02 2.50e+03 pdb=" O ALA A 374 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 375 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 374 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA a 374 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA a 374 " -0.033 2.00e-02 2.50e+03 pdb=" N THR a 375 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 373 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C HIS A 373 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS A 373 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 374 " -0.025 2.00e-02 2.50e+03 ... (remaining 4945 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 8482 2.82 - 3.40: 33370 3.40 - 3.98: 57533 3.98 - 4.56: 81369 4.56 - 5.14: 121687 Nonbonded interactions: 302441 Sorted by model distance: nonbonded pdb=" O TYR A 767 " pdb=" OG1 THR A 771 " model vdw 2.238 2.440 nonbonded pdb=" O GLN d 155 " pdb=" OG1 THR d 159 " model vdw 2.242 2.440 nonbonded pdb=" O GLN D 155 " pdb=" OG1 THR D 159 " model vdw 2.243 2.440 nonbonded pdb=" O TYR a 767 " pdb=" OG1 THR a 771 " model vdw 2.249 2.440 nonbonded pdb=" O PHE A 315 " pdb=" OH TYR A 577 " model vdw 2.261 2.440 ... (remaining 302436 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 'a' } ncs_group { reference = (chain 'B' and resid 3 through 140) selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and resid 1 through 158) selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 3.650 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 84.020 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.250 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.008 0.184 30962 Z= 0.526 Angle : 1.135 15.316 41942 Z= 0.579 Chirality : 0.060 0.369 4988 Planarity : 0.009 0.063 4948 Dihedral : 12.510 174.609 10964 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.11), residues: 3716 helix: -1.12 (0.08), residues: 2742 sheet: -1.47 (0.57), residues: 70 loop : -3.36 (0.16), residues: 904 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 773 time to evaluate : 3.282 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 776 average time/residue: 1.1400 time to fit residues: 1083.2815 Evaluate side-chains 482 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 3.302 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3187 time to fit residues: 5.3816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 320 GLN A 547 HIS A 702 GLN A 733 HIS C 102 HIS D 155 GLN D 266 HIS ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 158 HIS a 191 GLN a 610 ASN a 733 HIS ** a 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30962 Z= 0.263 Angle : 0.683 8.663 41942 Z= 0.355 Chirality : 0.044 0.209 4988 Planarity : 0.006 0.057 4948 Dihedral : 12.200 144.990 4650 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 3.64 % Allowed : 11.49 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.40 (0.13), residues: 3716 helix: 0.65 (0.10), residues: 2728 sheet: -0.40 (0.57), residues: 90 loop : -3.08 (0.17), residues: 898 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 532 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 42 residues processed: 594 average time/residue: 1.1121 time to fit residues: 813.3368 Evaluate side-chains 521 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 479 time to evaluate : 3.418 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 23 residues processed: 19 average time/residue: 0.6754 time to fit residues: 22.2760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 357 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 GLN a 372 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30962 Z= 0.207 Angle : 0.627 10.113 41942 Z= 0.324 Chirality : 0.042 0.233 4988 Planarity : 0.005 0.054 4948 Dihedral : 11.507 152.000 4650 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.28 % Allowed : 13.56 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.42 (0.14), residues: 3716 helix: 1.26 (0.10), residues: 2722 sheet: -0.11 (0.59), residues: 90 loop : -2.81 (0.17), residues: 904 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 526 time to evaluate : 3.560 Fit side-chains revert: symmetry clash outliers start: 134 outliers final: 57 residues processed: 603 average time/residue: 1.0701 time to fit residues: 801.9555 Evaluate side-chains 519 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 462 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 35 residues processed: 23 average time/residue: 0.5819 time to fit residues: 23.5497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 351 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN A 727 GLN D 3 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 138 ASN a 191 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30962 Z= 0.270 Angle : 0.660 9.726 41942 Z= 0.339 Chirality : 0.043 0.249 4988 Planarity : 0.005 0.056 4948 Dihedral : 11.353 155.144 4650 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.34 % Allowed : 14.58 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.67 (0.14), residues: 3716 helix: 1.41 (0.10), residues: 2740 sheet: -0.05 (0.59), residues: 90 loop : -2.62 (0.18), residues: 886 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 483 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 72 residues processed: 555 average time/residue: 1.0914 time to fit residues: 748.4055 Evaluate side-chains 522 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 450 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 38 residues processed: 34 average time/residue: 0.6551 time to fit residues: 34.9626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 243 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 727 GLN b 96 HIS ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30962 Z= 0.183 Angle : 0.598 12.479 41942 Z= 0.307 Chirality : 0.041 0.240 4988 Planarity : 0.005 0.056 4948 Dihedral : 10.849 159.493 4650 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.67 % Allowed : 15.67 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.96 (0.14), residues: 3716 helix: 1.62 (0.10), residues: 2742 sheet: -0.16 (0.59), residues: 94 loop : -2.50 (0.19), residues: 880 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 506 time to evaluate : 3.567 Fit side-chains revert: symmetry clash outliers start: 115 outliers final: 55 residues processed: 576 average time/residue: 0.9889 time to fit residues: 704.0807 Evaluate side-chains 513 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 458 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 37 residues processed: 19 average time/residue: 0.5441 time to fit residues: 17.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 352 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 3 ASN d 303 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30962 Z= 0.203 Angle : 0.612 13.696 41942 Z= 0.312 Chirality : 0.041 0.237 4988 Planarity : 0.005 0.048 4948 Dihedral : 10.701 161.003 4650 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.29 % Allowed : 17.04 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3716 helix: 1.67 (0.10), residues: 2746 sheet: -0.06 (0.59), residues: 94 loop : -2.42 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 479 time to evaluate : 3.548 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 64 residues processed: 540 average time/residue: 1.0997 time to fit residues: 735.6541 Evaluate side-chains 519 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 455 time to evaluate : 3.062 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 40 residues processed: 26 average time/residue: 0.5248 time to fit residues: 24.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30962 Z= 0.270 Angle : 0.658 13.257 41942 Z= 0.335 Chirality : 0.043 0.240 4988 Planarity : 0.005 0.047 4948 Dihedral : 10.873 162.284 4650 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.29 % Allowed : 17.29 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.99 (0.14), residues: 3716 helix: 1.60 (0.10), residues: 2750 sheet: -0.07 (0.58), residues: 94 loop : -2.40 (0.19), residues: 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 472 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 65 residues processed: 533 average time/residue: 1.0544 time to fit residues: 697.0719 Evaluate side-chains 512 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 447 time to evaluate : 3.300 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 44 residues processed: 22 average time/residue: 0.5556 time to fit residues: 21.9623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 223 optimal weight: 40.0000 chunk 239 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30962 Z= 0.311 Angle : 0.695 10.819 41942 Z= 0.355 Chirality : 0.045 0.343 4988 Planarity : 0.005 0.049 4948 Dihedral : 11.145 164.950 4650 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.06 % Allowed : 17.65 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.85 (0.14), residues: 3716 helix: 1.48 (0.10), residues: 2740 sheet: -0.09 (0.57), residues: 94 loop : -2.35 (0.19), residues: 882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 474 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 59 residues processed: 534 average time/residue: 1.1269 time to fit residues: 745.4367 Evaluate side-chains 511 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 452 time to evaluate : 3.417 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 42 residues processed: 18 average time/residue: 0.6372 time to fit residues: 20.5406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 295 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 325 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30962 Z= 0.204 Angle : 0.647 14.521 41942 Z= 0.327 Chirality : 0.042 0.308 4988 Planarity : 0.005 0.057 4948 Dihedral : 10.841 169.561 4650 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.65 % Allowed : 18.19 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3716 helix: 1.63 (0.10), residues: 2754 sheet: 0.03 (0.57), residues: 94 loop : -2.33 (0.20), residues: 868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 486 time to evaluate : 3.602 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 58 residues processed: 547 average time/residue: 1.1189 time to fit residues: 759.8138 Evaluate side-chains 518 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 460 time to evaluate : 3.255 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 49 residues processed: 12 average time/residue: 0.7725 time to fit residues: 17.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 20.0000 chunk 345 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 chunk 362 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 GLN a 389 HIS a 702 GLN c 96 GLN d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30962 Z= 0.322 Angle : 0.727 15.126 41942 Z= 0.367 Chirality : 0.045 0.276 4988 Planarity : 0.005 0.057 4948 Dihedral : 11.118 171.753 4650 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.27 % Allowed : 19.24 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.87 (0.14), residues: 3716 helix: 1.48 (0.10), residues: 2752 sheet: -0.01 (0.57), residues: 94 loop : -2.34 (0.20), residues: 870 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 473 time to evaluate : 3.341 Fit side-chains revert: symmetry clash outliers start: 71 outliers final: 52 residues processed: 523 average time/residue: 1.1305 time to fit residues: 730.5763 Evaluate side-chains 509 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 457 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 9 average time/residue: 0.6200 time to fit residues: 12.4649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 296 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN c 96 GLN d 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119904 restraints weight = 43099.766| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.90 r_work: 0.3380 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30962 Z= 0.202 Angle : 0.658 13.922 41942 Z= 0.333 Chirality : 0.042 0.339 4988 Planarity : 0.005 0.062 4948 Dihedral : 10.807 177.242 4650 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.85 % Allowed : 19.75 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3716 helix: 1.70 (0.10), residues: 2736 sheet: 0.00 (0.57), residues: 94 loop : -2.30 (0.20), residues: 886 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: