Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 22:51:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwb_24713/04_2023/7rwb_24713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwb_24713/04_2023/7rwb_24713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwb_24713/04_2023/7rwb_24713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwb_24713/04_2023/7rwb_24713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwb_24713/04_2023/7rwb_24713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwb_24713/04_2023/7rwb_24713.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.074 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 90 5.16 5 C 15450 2.51 5 N 4140 2.21 5 O 4282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23962 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4662 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 22, 'TRANS': 589} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 5, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3512 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 26, 'TRANS': 530} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1153 Unresolved non-hydrogen dihedrals: 734 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 21, 'ASP:plan': 30, 'PHE:plan': 3, 'GLU:plan': 38, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 498 Chain: "M" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2692 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 299 Chain: "S" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1115 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "a" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4662 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 22, 'TRANS': 589} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 5, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 115 Chain: "b" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3512 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 26, 'TRANS': 530} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1153 Unresolved non-hydrogen dihedrals: 734 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 21, 'ASP:plan': 30, 'PHE:plan': 3, 'GLU:plan': 38, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 498 Chain: "m" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2692 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 299 Chain: "s" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1115 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 12.40, per 1000 atoms: 0.52 Number of scatterers: 23962 At special positions: 0 Unit cell: (132.09, 187.59, 124.32, 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 90 16.00 O 4282 8.00 N 4140 7.00 C 15450 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: 9.40 Conformation dependent library (CDL) restraints added in 3.7 seconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 14 sheets defined 63.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.549A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 removed outlier: 3.674A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.891A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 124 through 139 removed outlier: 3.969A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.745A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.862A pdb=" N HIS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.891A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.008A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.083A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.936A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 6.004A pdb=" N PHE A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.833A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.630A pdb=" N GLN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.645A pdb=" N ILE A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.801A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.784A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.683A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.592A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.914A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.711A pdb=" N ALA A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.507A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.607A pdb=" N ILE B 85 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET B 86 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.862A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.567A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.888A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 4.001A pdb=" N GLN B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.845A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.890A pdb=" N VAL B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.544A pdb=" N GLN B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.538A pdb=" N ARG B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.693A pdb=" N LEU B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.616A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.176A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.517A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.522A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 133 removed outlier: 3.632A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.584A pdb=" N ALA M 382 " --> pdb=" O LYS M 379 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG M 383 " --> pdb=" O LYS M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.660A pdb=" N LYS S 28 " --> pdb=" O ASP S 24 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 118 Processing helix chain 'S' and resid 128 through 138 Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.549A pdb=" N VAL a 15 " --> pdb=" O ARG a 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN a 22 " --> pdb=" O SER a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 45 removed outlier: 3.674A pdb=" N GLU a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 69 removed outlier: 3.890A pdb=" N GLY a 69 " --> pdb=" O ILE a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 81 Processing helix chain 'a' and resid 87 through 101 Processing helix chain 'a' and resid 105 through 121 Processing helix chain 'a' and resid 124 through 139 removed outlier: 3.970A pdb=" N VAL a 138 " --> pdb=" O CYS a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 148 Processing helix chain 'a' and resid 150 through 156 Processing helix chain 'a' and resid 161 through 179 Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.745A pdb=" N VAL a 183 " --> pdb=" O PRO a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 188 through 196 removed outlier: 3.862A pdb=" N HIS a 194 " --> pdb=" O SER a 190 " (cutoff:3.500A) Processing helix chain 'a' and resid 201 through 218 Processing helix chain 'a' and resid 219 through 223 removed outlier: 3.890A pdb=" N LYS a 223 " --> pdb=" O GLU a 220 " (cutoff:3.500A) Processing helix chain 'a' and resid 224 through 238 removed outlier: 4.008A pdb=" N LEU a 228 " --> pdb=" O THR a 224 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR a 238 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 246 No H-bonds generated for 'chain 'a' and resid 244 through 246' Processing helix chain 'a' and resid 254 through 267 Processing helix chain 'a' and resid 273 through 293 Processing helix chain 'a' and resid 299 through 321 removed outlier: 4.083A pdb=" N SER a 303 " --> pdb=" O LYS a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 323 through 338 Processing helix chain 'a' and resid 342 through 357 removed outlier: 3.936A pdb=" N ARG a 346 " --> pdb=" O GLU a 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 358 through 361 removed outlier: 6.004A pdb=" N PHE a 361 " --> pdb=" O SER a 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 358 through 361' Processing helix chain 'a' and resid 362 through 368 Processing helix chain 'a' and resid 369 through 380 removed outlier: 3.833A pdb=" N GLU a 380 " --> pdb=" O ALA a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 383 through 396 removed outlier: 3.630A pdb=" N GLN a 387 " --> pdb=" O VAL a 383 " (cutoff:3.500A) Processing helix chain 'a' and resid 401 through 416 removed outlier: 3.644A pdb=" N ILE a 405 " --> pdb=" O ASN a 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR a 415 " --> pdb=" O SER a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 417 through 419 No H-bonds generated for 'chain 'a' and resid 417 through 419' Processing helix chain 'a' and resid 420 through 435 Processing helix chain 'a' and resid 438 through 453 removed outlier: 3.801A pdb=" N TYR a 442 " --> pdb=" O ASP a 438 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 473 removed outlier: 3.784A pdb=" N ASP a 473 " --> pdb=" O VAL a 469 " (cutoff:3.500A) Processing helix chain 'a' and resid 475 through 488 removed outlier: 3.683A pdb=" N GLN a 488 " --> pdb=" O PHE a 484 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 508 Processing helix chain 'a' and resid 514 through 517 Processing helix chain 'a' and resid 518 through 531 removed outlier: 3.593A pdb=" N HIS a 531 " --> pdb=" O HIS a 527 " (cutoff:3.500A) Processing helix chain 'a' and resid 534 through 552 removed outlier: 3.914A pdb=" N ASN a 550 " --> pdb=" O ILE a 546 " (cutoff:3.500A) Processing helix chain 'a' and resid 555 through 564 Processing helix chain 'a' and resid 565 through 570 Processing helix chain 'a' and resid 573 through 590 removed outlier: 3.710A pdb=" N ALA a 590 " --> pdb=" O LEU a 586 " (cutoff:3.500A) Processing helix chain 'a' and resid 594 through 599 Processing helix chain 'a' and resid 610 through 620 removed outlier: 3.507A pdb=" N ALA a 614 " --> pdb=" O SER a 610 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 44 Processing helix chain 'b' and resid 47 through 49 No H-bonds generated for 'chain 'b' and resid 47 through 49' Processing helix chain 'b' and resid 50 through 58 Processing helix chain 'b' and resid 62 through 78 Processing helix chain 'b' and resid 81 through 86 removed outlier: 3.607A pdb=" N ILE b 85 " --> pdb=" O ASP b 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET b 86 " --> pdb=" O MET b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 96 Processing helix chain 'b' and resid 99 through 112 removed outlier: 3.862A pdb=" N CYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 129 removed outlier: 4.567A pdb=" N GLU b 124 " --> pdb=" O GLU b 120 " (cutoff:3.500A) Proline residue: b 125 - end of helix Processing helix chain 'b' and resid 134 through 151 removed outlier: 3.888A pdb=" N ASP b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE b 151 " --> pdb=" O LYS b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 170 removed outlier: 4.001A pdb=" N GLN b 159 " --> pdb=" O MET b 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 188 Processing helix chain 'b' and resid 202 through 213 Processing helix chain 'b' and resid 215 through 227 Processing helix chain 'b' and resid 233 through 244 removed outlier: 3.845A pdb=" N ALA b 237 " --> pdb=" O ASP b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 266 removed outlier: 3.890A pdb=" N VAL b 256 " --> pdb=" O ASN b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 276 through 291 Proline residue: b 286 - end of helix Processing helix chain 'b' and resid 295 through 313 Processing helix chain 'b' and resid 320 through 325 Processing helix chain 'b' and resid 331 through 345 Processing helix chain 'b' and resid 350 through 362 Processing helix chain 'b' and resid 366 through 384 Processing helix chain 'b' and resid 387 through 400 removed outlier: 3.545A pdb=" N GLN b 400 " --> pdb=" O LEU b 396 " (cutoff:3.500A) Processing helix chain 'b' and resid 403 through 419 removed outlier: 3.538A pdb=" N ARG b 419 " --> pdb=" O ARG b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 425 through 427 No H-bonds generated for 'chain 'b' and resid 425 through 427' Processing helix chain 'b' and resid 428 through 435 removed outlier: 3.693A pdb=" N LEU b 432 " --> pdb=" O ILE b 428 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN b 435 " --> pdb=" O THR b 431 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 455 Processing helix chain 'b' and resid 461 through 470 Processing helix chain 'b' and resid 477 through 495 Processing helix chain 'b' and resid 502 through 513 Processing helix chain 'b' and resid 516 through 531 Processing helix chain 'b' and resid 533 through 541 Processing helix chain 'b' and resid 556 through 565 removed outlier: 3.616A pdb=" N CYS b 565 " --> pdb=" O ASP b 561 " (cutoff:3.500A) Processing helix chain 'b' and resid 569 through 575 removed outlier: 4.176A pdb=" N VAL b 573 " --> pdb=" O SER b 569 " (cutoff:3.500A) Processing helix chain 'b' and resid 577 through 581 Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.517A pdb=" N VAL m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 94 removed outlier: 3.522A pdb=" N VAL m 78 " --> pdb=" O ASN m 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE m 79 " --> pdb=" O ALA m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 104 Processing helix chain 'm' and resid 104 through 115 Processing helix chain 'm' and resid 125 through 133 removed outlier: 3.632A pdb=" N THR m 131 " --> pdb=" O GLY m 127 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE m 132 " --> pdb=" O ALA m 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 379 through 383 removed outlier: 3.584A pdb=" N ALA m 382 " --> pdb=" O LYS m 379 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG m 383 " --> pdb=" O LYS m 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 379 through 383' Processing helix chain 'm' and resid 414 through 418 Processing helix chain 's' and resid 24 through 42 removed outlier: 3.661A pdb=" N LYS s 28 " --> pdb=" O ASP s 24 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN s 29 " --> pdb=" O ASP s 25 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL s 41 " --> pdb=" O ALA s 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG s 42 " --> pdb=" O VAL s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 77 through 96 Processing helix chain 's' and resid 99 through 106 Processing helix chain 's' and resid 106 through 118 Processing helix chain 's' and resid 128 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 18 removed outlier: 7.047A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU M 5 " --> pdb=" O SER M 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.796A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 270 through 279 removed outlier: 6.337A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU M 184 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS M 195 " --> pdb=" O ASN M 182 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 263 through 265 removed outlier: 3.711A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE M 265 " --> pdb=" O CYS M 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS M 212 " --> pdb=" O PHE M 265 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU M 211 " --> pdb=" O PHE M 407 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE M 407 " --> pdb=" O GLU M 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.851A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 367 " --> pdb=" O ILE M 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU M 369 " --> pdb=" O GLN M 334 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 14 through 19 removed outlier: 7.069A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS S 56 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL S 50 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 248 through 249 Processing sheet with id=AA9, first strand: chain 'm' and resid 14 through 18 removed outlier: 7.046A pdb=" N ILE m 7 " --> pdb=" O LEU m 15 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER m 17 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU m 5 " --> pdb=" O SER m 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 116 through 117 removed outlier: 3.796A pdb=" N ASP m 117 " --> pdb=" O TYR m 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 270 through 279 removed outlier: 6.337A pdb=" N GLU m 271 " --> pdb=" O SER m 204 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER m 204 " --> pdb=" O GLU m 271 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU m 273 " --> pdb=" O MET m 202 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET m 202 " --> pdb=" O GLU m 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET m 275 " --> pdb=" O VAL m 200 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER m 193 " --> pdb=" O LEU m 184 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU m 184 " --> pdb=" O SER m 193 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS m 195 " --> pdb=" O ASN m 182 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU m 173 " --> pdb=" O TRP m 421 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG m 423 " --> pdb=" O LEU m 173 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU m 175 " --> pdb=" O ARG m 423 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE m 425 " --> pdb=" O LEU m 175 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL m 177 " --> pdb=" O ILE m 425 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG m 427 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU m 179 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY m 429 " --> pdb=" O GLU m 179 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL m 181 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR m 431 " --> pdb=" O VAL m 181 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU m 183 " --> pdb=" O TYR m 431 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR m 433 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET m 185 " --> pdb=" O THR m 433 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG m 427 " --> pdb=" O VAL m 392 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL m 392 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY m 429 " --> pdb=" O PHE m 390 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE m 390 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR m 431 " --> pdb=" O MET m 388 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER m 387 " --> pdb=" O ARG m 323 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU m 391 " --> pdb=" O LYS m 319 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS m 319 " --> pdb=" O GLU m 391 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU m 316 " --> pdb=" O ALA m 359 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA m 359 " --> pdb=" O LEU m 316 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN m 318 " --> pdb=" O ARG m 357 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG m 357 " --> pdb=" O GLN m 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 263 through 265 removed outlier: 3.711A pdb=" N ILE m 263 " --> pdb=" O PHE m 214 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE m 265 " --> pdb=" O CYS m 212 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS m 212 " --> pdb=" O PHE m 265 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU m 211 " --> pdb=" O PHE m 407 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE m 407 " --> pdb=" O GLU m 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 287 through 294 removed outlier: 3.851A pdb=" N SER m 364 " --> pdb=" O ILE m 307 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 367 " --> pdb=" O ILE m 336 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU m 369 " --> pdb=" O GLN m 334 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN m 334 " --> pdb=" O GLU m 369 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY m 332 " --> pdb=" O GLU m 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 's' and resid 14 through 19 removed outlier: 7.069A pdb=" N THR s 14 " --> pdb=" O ASN s 9 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN s 9 " --> pdb=" O THR s 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU s 16 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS s 70 " --> pdb=" O ARG s 3 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE s 5 " --> pdb=" O CYS s 68 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS s 68 " --> pdb=" O ILE s 5 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE s 7 " --> pdb=" O TYR s 66 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR s 66 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS s 56 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL s 50 " --> pdb=" O ILE s 57 " (cutoff:3.500A) 1544 hydrogen bonds defined for protein. 4512 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: 8.29 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7906 1.34 - 1.46: 4542 1.46 - 1.58: 11800 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 24388 Sorted by residual: bond pdb=" N LEU B 199 " pdb=" CA LEU B 199 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.90e-01 bond pdb=" N LEU b 199 " pdb=" CA LEU b 199 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.90e-01 bond pdb=" C GLN b 202 " pdb=" O GLN b 202 " ideal model delta sigma weight residual 1.235 1.246 -0.011 1.26e-02 6.30e+03 7.02e-01 bond pdb=" CD LYS A 56 " pdb=" CE LYS A 56 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.80e-01 bond pdb=" C GLN B 202 " pdb=" O GLN B 202 " ideal model delta sigma weight residual 1.235 1.246 -0.010 1.26e-02 6.30e+03 6.79e-01 ... (remaining 24383 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.68: 578 106.68 - 113.50: 13963 113.50 - 120.32: 8382 120.32 - 127.14: 10279 127.14 - 133.97: 198 Bond angle restraints: 33400 Sorted by residual: angle pdb=" N VAL a 555 " pdb=" CA VAL a 555 " pdb=" C VAL a 555 " ideal model delta sigma weight residual 112.29 107.75 4.54 9.40e-01 1.13e+00 2.33e+01 angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 112.29 107.80 4.49 9.40e-01 1.13e+00 2.28e+01 angle pdb=" C SER A 591 " pdb=" N THR A 592 " pdb=" CA THR A 592 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C SER a 591 " pdb=" N THR a 592 " pdb=" CA THR a 592 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C PRO B 201 " pdb=" N GLN B 202 " pdb=" CA GLN B 202 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.90e+00 ... (remaining 33395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 13452 17.76 - 35.51: 920 35.51 - 53.27: 146 53.27 - 71.03: 30 71.03 - 88.78: 12 Dihedral angle restraints: 14560 sinusoidal: 4470 harmonic: 10090 Sorted by residual: dihedral pdb=" CA SER A 458 " pdb=" C SER A 458 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER a 458 " pdb=" C SER a 458 " pdb=" N GLU a 459 " pdb=" CA GLU a 459 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS A 378 " pdb=" C LYS A 378 " pdb=" N THR A 379 " pdb=" CA THR A 379 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 14557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2848 0.035 - 0.070: 994 0.070 - 0.106: 250 0.106 - 0.141: 74 0.141 - 0.176: 4 Chirality restraints: 4170 Sorted by residual: chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB THR a 238 " pdb=" CA THR a 238 " pdb=" OG1 THR a 238 " pdb=" CG2 THR a 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 4167 not shown) Planarity restraints: 4260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL m 392 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO m 393 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO m 393 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO m 393 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 392 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO M 393 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO M 393 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 393 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 270 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.020 5.00e-02 4.00e+02 ... (remaining 4257 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 217 2.66 - 3.22: 23126 3.22 - 3.78: 36709 3.78 - 4.34: 45125 4.34 - 4.90: 76723 Nonbonded interactions: 181900 Sorted by model distance: nonbonded pdb=" OD1 ASP a 417 " pdb=" OG SER a 419 " model vdw 2.103 2.440 nonbonded pdb=" OD1 ASP A 417 " pdb=" OG SER A 419 " model vdw 2.103 2.440 nonbonded pdb=" OH TYR A 95 " pdb=" OD2 ASP A 119 " model vdw 2.194 2.440 nonbonded pdb=" OH TYR a 95 " pdb=" OD2 ASP a 119 " model vdw 2.194 2.440 nonbonded pdb=" O VAL b 301 " pdb=" ND2 ASN b 305 " model vdw 2.217 2.520 ... (remaining 181895 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' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'S' selection = chain 's' } 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 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: 3.940 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: 0.020 Extract box with map and model: 15.370 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 59.060 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 0.032 24388 Z= 0.174 Angle : 0.533 9.092 33400 Z= 0.300 Chirality : 0.040 0.176 4170 Planarity : 0.003 0.038 4260 Dihedral : 12.887 88.783 7972 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer Outliers : 0.10 % 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: 0.92 (0.15), residues: 3380 helix: 1.90 (0.12), residues: 1934 sheet: -0.13 (0.29), residues: 330 loop : -1.53 (0.17), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.3282 time to fit residues: 133.3755 Evaluate side-chains 184 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 5.9990 chunk 256 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 264 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 197 optimal weight: 0.0010 chunk 306 optimal weight: 30.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 ASN m 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 24388 Z= 0.207 Angle : 0.508 11.937 33400 Z= 0.267 Chirality : 0.040 0.162 4170 Planarity : 0.004 0.039 4260 Dihedral : 3.654 18.464 3604 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.00 % Rotamer Outliers : 1.00 % 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: 0.99 (0.15), residues: 3380 helix: 1.92 (0.12), residues: 1954 sheet: -0.14 (0.29), residues: 332 loop : -1.48 (0.18), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 203 average time/residue: 0.3094 time to fit residues: 105.5205 Evaluate side-chains 187 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2293 time to fit residues: 8.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 307 optimal weight: 6.9990 chunk 332 optimal weight: 0.6980 chunk 273 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 246 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 ASN m 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24388 Z= 0.197 Angle : 0.487 10.083 33400 Z= 0.257 Chirality : 0.039 0.154 4170 Planarity : 0.003 0.037 4260 Dihedral : 3.627 18.959 3604 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.81 % 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: 0.97 (0.15), residues: 3380 helix: 1.94 (0.12), residues: 1958 sheet: -0.12 (0.29), residues: 324 loop : -1.59 (0.18), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 215 average time/residue: 0.3197 time to fit residues: 115.6562 Evaluate side-chains 188 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 2.933 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2186 time to fit residues: 8.5509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 206 optimal weight: 0.5980 chunk 308 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24388 Z= 0.230 Angle : 0.503 9.839 33400 Z= 0.265 Chirality : 0.040 0.150 4170 Planarity : 0.003 0.037 4260 Dihedral : 3.678 19.671 3604 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.67 % 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: 0.97 (0.15), residues: 3380 helix: 1.94 (0.12), residues: 1960 sheet: -0.14 (0.28), residues: 322 loop : -1.57 (0.18), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 205 average time/residue: 0.3119 time to fit residues: 108.2250 Evaluate side-chains 193 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2510 time to fit residues: 9.8780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 278 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN M 38 HIS M 122 GLN a 467 GLN ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 GLN m 38 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 24388 Z= 0.420 Angle : 0.645 9.253 33400 Z= 0.333 Chirality : 0.043 0.156 4170 Planarity : 0.004 0.040 4260 Dihedral : 4.147 23.011 3604 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 1.87 % 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: 0.52 (0.15), residues: 3380 helix: 1.55 (0.12), residues: 1958 sheet: -0.34 (0.28), residues: 322 loop : -1.68 (0.18), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 2.888 Fit side-chains outliers start: 39 outliers final: 18 residues processed: 225 average time/residue: 0.2957 time to fit residues: 114.3021 Evaluate side-chains 205 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.835 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2169 time to fit residues: 11.1503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 191 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS a 401 ASN m 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 24388 Z= 0.265 Angle : 0.538 9.112 33400 Z= 0.283 Chirality : 0.041 0.210 4170 Planarity : 0.004 0.042 4260 Dihedral : 4.003 22.742 3604 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.34 % 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: 0.71 (0.15), residues: 3380 helix: 1.72 (0.12), residues: 1946 sheet: -0.33 (0.28), residues: 326 loop : -1.59 (0.18), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 3.015 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 211 average time/residue: 0.3182 time to fit residues: 112.3940 Evaluate side-chains 197 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 2.971 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2304 time to fit residues: 8.7654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 chunk 275 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 325 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 198 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24388 Z= 0.213 Angle : 0.509 8.831 33400 Z= 0.269 Chirality : 0.040 0.174 4170 Planarity : 0.003 0.040 4260 Dihedral : 3.897 21.102 3604 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.91 % 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: 0.85 (0.15), residues: 3380 helix: 1.84 (0.12), residues: 1946 sheet: -0.22 (0.28), residues: 326 loop : -1.57 (0.18), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 2.832 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 205 average time/residue: 0.3253 time to fit residues: 112.8682 Evaluate side-chains 190 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2312 time to fit residues: 6.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 64 optimal weight: 0.0470 chunk 63 optimal weight: 8.9990 chunk 207 optimal weight: 0.0870 chunk 221 optimal weight: 0.4980 chunk 161 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN a 577 GLN m 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 24388 Z= 0.163 Angle : 0.476 8.694 33400 Z= 0.254 Chirality : 0.039 0.159 4170 Planarity : 0.003 0.039 4260 Dihedral : 3.734 19.632 3604 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3380 helix: 1.99 (0.12), residues: 1950 sheet: -0.21 (0.28), residues: 334 loop : -1.48 (0.18), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 2.863 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 209 average time/residue: 0.3089 time to fit residues: 109.1878 Evaluate side-chains 194 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 2.976 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2257 time to fit residues: 7.6123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 93 optimal weight: 0.0270 chunk 274 optimal weight: 0.9980 chunk 287 optimal weight: 0.0770 chunk 302 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN M 38 HIS a 113 ASN m 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24388 Z= 0.194 Angle : 0.497 9.865 33400 Z= 0.262 Chirality : 0.040 0.150 4170 Planarity : 0.003 0.038 4260 Dihedral : 3.713 19.415 3604 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3380 helix: 1.99 (0.12), residues: 1958 sheet: -0.14 (0.28), residues: 334 loop : -1.42 (0.18), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 2.943 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 197 average time/residue: 0.3207 time to fit residues: 106.2676 Evaluate side-chains 192 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2069 time to fit residues: 6.7512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.6980 chunk 321 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 chunk 309 optimal weight: 0.4980 chunk 268 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 207 optimal weight: 0.1980 chunk 164 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24388 Z= 0.194 Angle : 0.497 9.527 33400 Z= 0.262 Chirality : 0.040 0.147 4170 Planarity : 0.003 0.039 4260 Dihedral : 3.713 19.595 3604 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3380 helix: 2.01 (0.12), residues: 1958 sheet: -0.09 (0.28), residues: 334 loop : -1.41 (0.18), residues: 1088 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 2.928 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 188 average time/residue: 0.3291 time to fit residues: 104.1764 Evaluate side-chains 182 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 2.804 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3119 time to fit residues: 4.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.5980 chunk 285 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 268 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 275 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.174191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.171918 restraints weight = 40554.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.171531 restraints weight = 59315.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.170936 restraints weight = 63331.407| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24388 Z= 0.181 Angle : 0.491 9.654 33400 Z= 0.259 Chirality : 0.039 0.146 4170 Planarity : 0.003 0.039 4260 Dihedral : 3.672 18.849 3604 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3380 helix: 2.05 (0.12), residues: 1958 sheet: -0.12 (0.27), residues: 344 loop : -1.38 (0.18), residues: 1078 =============================================================================== Job complete usr+sys time: 3436.41 seconds wall clock time: 64 minutes 20.52 seconds (3860.52 seconds total)