Starting phenix.real_space_refine (version: dev) on Fri Mar 17 13:11:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/03_2023/6d7t_7825_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/03_2023/6d7t_7825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/03_2023/6d7t_7825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/03_2023/6d7t_7825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/03_2023/6d7t_7825_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/03_2023/6d7t_7825_updated.pdb" } resolution = 4.44 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= 0.009 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 Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19654 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "B" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "C" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "D" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' CA': 2, 'FZ4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="CA CA A 802 " occ=0.25 residue: pdb="CA CA A 803 " occ=0.25 Time building chain proxies: 11.55, per 1000 atoms: 0.59 Number of scatterers: 19654 At special positions: 0 Unit cell: (132.98, 132.98, 123.22, 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) Ca 2 19.99 S 160 16.00 O 3460 8.00 N 3324 7.00 C 12704 6.00 B 4 5.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 4 sheets defined 52.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.591A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.903A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 132 through 139 removed outlier: 3.883A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.842A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.532A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 213 through 220 removed outlier: 4.369A pdb=" N ASN A 217 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.590A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.554A pdb=" N MET A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 384 through 410 removed outlier: 3.949A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.606A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 425 through 445 removed outlier: 3.722A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.772A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.745A pdb=" N ARG A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 490 through 513 removed outlier: 3.693A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 removed outlier: 3.695A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 566 removed outlier: 3.660A pdb=" N ILE A 557 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 removed outlier: 4.003A pdb=" N MET A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 607 removed outlier: 3.811A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 removed outlier: 3.591A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.902A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 132 through 139 removed outlier: 3.883A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.843A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.531A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 213 through 220 removed outlier: 4.369A pdb=" N ASN B 217 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 218 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.590A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 313 through 322 Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.554A pdb=" N MET B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 384 through 410 removed outlier: 3.949A pdb=" N VAL B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.606A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 425 through 445 removed outlier: 3.722A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.771A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.745A pdb=" N ARG B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'B' and resid 490 through 513 removed outlier: 3.693A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.695A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 566 removed outlier: 3.660A pdb=" N ILE B 557 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE B 564 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 581 removed outlier: 4.003A pdb=" N MET B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 607 removed outlier: 3.811A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.590A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.902A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 132 through 139 removed outlier: 3.882A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.842A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.532A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 213 through 220 removed outlier: 4.370A pdb=" N ASN C 217 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C 218 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.590A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 313 through 322 Processing helix chain 'C' and resid 326 through 348 removed outlier: 3.553A pdb=" N MET C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 384 through 410 removed outlier: 3.950A pdb=" N VAL C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU C 403 " --> pdb=" O ILE C 399 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.607A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 425 through 445 removed outlier: 3.723A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 removed outlier: 3.772A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.745A pdb=" N ARG C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 486 Processing helix chain 'C' and resid 490 through 513 removed outlier: 3.693A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 removed outlier: 3.695A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 566 removed outlier: 3.660A pdb=" N ILE C 557 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR C 559 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE C 564 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 removed outlier: 4.003A pdb=" N MET C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.810A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.590A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 65 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.902A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 132 through 139 removed outlier: 3.883A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.842A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.531A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 213 through 220 removed outlier: 4.369A pdb=" N ASN D 217 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 218 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 3.591A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 261 Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 313 through 322 Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.554A pdb=" N MET D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 384 through 410 removed outlier: 3.949A pdb=" N VAL D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.607A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 425 through 445 removed outlier: 3.723A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.771A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.745A pdb=" N ARG D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 486 Processing helix chain 'D' and resid 490 through 513 removed outlier: 3.693A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 removed outlier: 3.695A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 removed outlier: 3.659A pdb=" N ILE D 557 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR D 559 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE D 564 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 581 removed outlier: 4.004A pdb=" N MET D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 607 removed outlier: 3.810A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.622A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.623A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.622A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.622A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 2831 1.25 - 1.39: 5305 1.39 - 1.54: 11174 1.54 - 1.68: 521 1.68 - 1.82: 273 Bond restraints: 20104 Sorted by residual: bond pdb=" C PRO D 544 " pdb=" N ALA D 545 " ideal model delta sigma weight residual 1.331 1.727 -0.396 1.23e-02 6.61e+03 1.04e+03 bond pdb=" C ILE D 540 " pdb=" N ILE D 541 " ideal model delta sigma weight residual 1.335 1.552 -0.217 1.27e-02 6.20e+03 2.92e+02 bond pdb=" C ILE C 540 " pdb=" N ILE C 541 " ideal model delta sigma weight residual 1.332 1.103 0.229 1.73e-02 3.34e+03 1.76e+02 bond pdb=" C ILE B 540 " pdb=" N ILE B 541 " ideal model delta sigma weight residual 1.332 1.510 -0.178 1.73e-02 3.34e+03 1.06e+02 bond pdb=" C ILE A 540 " pdb=" N ILE A 541 " ideal model delta sigma weight residual 1.332 1.510 -0.178 1.73e-02 3.34e+03 1.06e+02 ... (remaining 20099 not shown) Histogram of bond angle deviations from ideal: 95.15 - 102.98: 167 102.98 - 110.81: 6676 110.81 - 118.63: 9227 118.63 - 126.46: 10796 126.46 - 134.29: 402 Bond angle restraints: 27268 Sorted by residual: angle pdb=" O PRO D 544 " pdb=" C PRO D 544 " pdb=" N ALA D 545 " ideal model delta sigma weight residual 123.03 110.57 12.46 1.06e+00 8.90e-01 1.38e+02 angle pdb=" C ILE D 540 " pdb=" N ILE D 541 " pdb=" CA ILE D 541 " ideal model delta sigma weight residual 120.13 102.63 17.50 1.58e+00 4.01e-01 1.23e+02 angle pdb=" CA ILE D 540 " pdb=" C ILE D 540 " pdb=" N ILE D 541 " ideal model delta sigma weight residual 116.60 102.58 14.02 1.45e+00 4.76e-01 9.35e+01 angle pdb=" CA PRO D 544 " pdb=" C PRO D 544 " pdb=" N ALA D 545 " ideal model delta sigma weight residual 116.01 128.14 -12.13 1.27e+00 6.20e-01 9.12e+01 angle pdb=" O ILE D 540 " pdb=" C ILE D 540 " pdb=" N ILE D 541 " ideal model delta sigma weight residual 122.57 132.50 -9.93 1.25e+00 6.40e-01 6.31e+01 ... (remaining 27263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 11736 35.95 - 71.89: 268 71.89 - 107.84: 4 107.84 - 143.78: 0 143.78 - 179.73: 4 Dihedral angle restraints: 12012 sinusoidal: 4868 harmonic: 7144 Sorted by residual: dihedral pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta harmonic sigma weight residual 180.00 142.43 37.57 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 142.46 37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA ASN D 129 " pdb=" C ASN D 129 " pdb=" N MET D 130 " pdb=" CA MET D 130 " ideal model delta harmonic sigma weight residual 180.00 142.51 37.49 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 12009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1720 0.049 - 0.097: 880 0.097 - 0.146: 379 0.146 - 0.195: 89 0.195 - 0.243: 24 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CA GLN D 370 " pdb=" N GLN D 370 " pdb=" C GLN D 370 " pdb=" CB GLN D 370 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLN C 370 " pdb=" N GLN C 370 " pdb=" C GLN C 370 " pdb=" CB GLN C 370 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLN B 370 " pdb=" N GLN B 370 " pdb=" C GLN B 370 " pdb=" CB GLN B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3089 not shown) Planarity restraints: 3448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 540 " -0.033 2.00e-02 2.50e+03 7.50e-02 5.62e+01 pdb=" C ILE D 540 " 0.129 2.00e-02 2.50e+03 pdb=" O ILE D 540 " -0.057 2.00e-02 2.50e+03 pdb=" N ILE D 541 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 544 " 0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C PRO C 544 " -0.112 2.00e-02 2.50e+03 pdb=" O PRO C 544 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA C 545 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C ASP C 223 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG C 224 " 0.015 2.00e-02 2.50e+03 ... (remaining 3445 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 245 2.58 - 3.16: 16778 3.16 - 3.74: 32476 3.74 - 4.32: 43590 4.32 - 4.90: 65087 Nonbonded interactions: 158176 Sorted by model distance: nonbonded pdb=" OD1 ASP D 542 " pdb="CA CA A 803 " model vdw 1.997 2.510 nonbonded pdb=" OD1 ASP C 542 " pdb="CA CA A 803 " model vdw 2.030 2.510 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.164 2.440 nonbonded pdb=" OG1 THR D 360 " pdb=" OG1 THR D 366 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR C 360 " pdb=" OG1 THR C 366 " model vdw 2.228 2.440 ... (remaining 158171 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' and (resid 28 through 638 or resid 801)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 S 160 5.16 5 B 4 2.79 5 C 12704 2.51 5 N 3324 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.820 Check model and map are aligned: 0.270 Process input model: 52.050 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.010 0.396 20104 Z= 0.683 Angle : 1.494 17.542 27268 Z= 0.799 Chirality : 0.068 0.243 3092 Planarity : 0.008 0.075 3448 Dihedral : 14.786 179.729 7396 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.71 % Favored : 88.75 % Rotamer Outliers : 5.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -5.38 (0.13), residues: 2436 helix: -3.93 (0.08), residues: 1208 sheet: -6.48 (0.12), residues: 56 loop : -2.92 (0.17), residues: 1172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 624 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 32 residues processed: 683 average time/residue: 0.3555 time to fit residues: 356.5445 Evaluate side-chains 460 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 428 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3310 time to fit residues: 19.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 0.0070 chunk 124 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN C 546 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 20104 Z= 0.207 Angle : 0.842 12.970 27268 Z= 0.413 Chirality : 0.045 0.171 3092 Planarity : 0.005 0.048 3448 Dihedral : 9.623 170.909 2692 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.88 % Favored : 91.95 % 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: -4.22 (0.15), residues: 2436 helix: -2.58 (0.12), residues: 1256 sheet: -6.42 (0.10), residues: 56 loop : -2.79 (0.18), residues: 1124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 624 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 624 average time/residue: 0.2956 time to fit residues: 284.6224 Evaluate side-chains 442 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 2.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 20104 Z= 0.267 Angle : 0.812 14.251 27268 Z= 0.404 Chirality : 0.044 0.180 3092 Planarity : 0.005 0.046 3448 Dihedral : 9.222 171.179 2692 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.46 % Favored : 91.38 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.16), residues: 2436 helix: -1.79 (0.13), residues: 1244 sheet: -6.43 (0.10), residues: 56 loop : -2.42 (0.18), residues: 1136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 558 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 561 average time/residue: 0.2866 time to fit residues: 254.7014 Evaluate side-chains 419 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 2.473 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2239 time to fit residues: 3.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 7.9990 chunk 166 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 0.0000 chunk 149 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 0.4980 chunk 116 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 20104 Z= 0.188 Angle : 0.787 14.512 27268 Z= 0.376 Chirality : 0.044 0.190 3092 Planarity : 0.004 0.048 3448 Dihedral : 8.556 155.806 2692 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.39 % Favored : 92.45 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.16), residues: 2436 helix: -1.38 (0.14), residues: 1200 sheet: -6.45 (0.10), residues: 56 loop : -2.20 (0.19), residues: 1180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 583 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 586 average time/residue: 0.3074 time to fit residues: 278.8691 Evaluate side-chains 444 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 442 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2273 time to fit residues: 4.1733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 201 optimal weight: 0.0980 chunk 163 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 118 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 20104 Z= 0.229 Angle : 0.797 13.271 27268 Z= 0.384 Chirality : 0.044 0.183 3092 Planarity : 0.004 0.054 3448 Dihedral : 8.085 142.907 2692 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.17), residues: 2436 helix: -0.99 (0.14), residues: 1192 sheet: -6.46 (0.10), residues: 56 loop : -2.28 (0.18), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 558 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 561 average time/residue: 0.2859 time to fit residues: 249.5335 Evaluate side-chains 446 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 443 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2722 time to fit residues: 4.4123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 0.0970 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 78 optimal weight: 0.0570 chunk 123 optimal weight: 0.6980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: