Starting phenix.real_space_refine (version: dev) on Wed Apr 6 08:47:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/04_2022/6d7t_7825_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/04_2022/6d7t_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_7825/04_2022/6d7t_7825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/04_2022/6d7t_7825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/04_2022/6d7t_7825_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/04_2022/6d7t_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 Convert atoms to be neutral 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-4553/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: 11.36, per 1000 atoms: 0.58 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: 9.02 Conformation dependent library (CDL) restraints added in 2.9 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: 2.16 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: 5.84 Time building geometry restraints manager: 9.50 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: 0.390 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: 3.490 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.160 Process input model: 52.760 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.100 ------------------------------------------------------------------------------- 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 : 11.64 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 : 2.317 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: 0.3286 time to fit residues: 330.8324 Evaluate side-chains 459 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 427 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3098 time to fit residues: 17.9504 ------------------------------------------------------------------------------- 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 483 GLN 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 483 GLN C 546 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20104 Z= 0.219 Angle : 0.850 13.098 27268 Z= 0.419 Chirality : 0.045 0.172 3092 Planarity : 0.005 0.049 3448 Dihedral : 9.728 171.527 2692 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.42 % Favored : 91.42 % 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: -4.29 (0.15), residues: 2436 helix: -2.65 (0.11), residues: 1284 sheet: -6.41 (0.10), residues: 56 loop : -2.80 (0.19), residues: 1096 *********************** 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 623 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 619 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 619 average time/residue: 0.2891 time to fit residues: 277.3688 Evaluate side-chains 438 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0930 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 239 optimal weight: 0.0470 chunk 197 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 596 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 20104 Z= 0.213 Angle : 0.803 13.935 27268 Z= 0.392 Chirality : 0.044 0.177 3092 Planarity : 0.005 0.047 3448 Dihedral : 9.086 166.384 2692 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.00 % Favored : 91.83 % Rotamer Outliers : 0.00 % 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: -3.51 (0.15), residues: 2436 helix: -1.93 (0.13), residues: 1268 sheet: -6.38 (0.10), residues: 56 loop : -2.52 (0.18), residues: 1112 *********************** 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 565 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 565 average time/residue: 0.2733 time to fit residues: 244.2267 Evaluate side-chains 426 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2085 ------------------------------------------------------------------------------- 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: 0.6980 chunk 115 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.0050 chunk 149 optimal weight: 0.1980 chunk 222 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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** ** 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 36 GLN ** 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 239 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 20104 Z= 0.190 Angle : 0.787 14.453 27268 Z= 0.377 Chirality : 0.044 0.182 3092 Planarity : 0.005 0.050 3448 Dihedral : 8.465 152.332 2692 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.84 % Favored : 92.04 % Rotamer Outliers : 0.00 % 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: -3.15 (0.16), residues: 2436 helix: -1.56 (0.13), residues: 1244 sheet: -6.42 (0.10), residues: 56 loop : -2.42 (0.18), residues: 1136 *********************** 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: 0 poor density : 586 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.2896 time to fit residues: 264.8725 Evaluate side-chains 452 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3022 ------------------------------------------------------------------------------- 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: 0.0670 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 0.0050 chunk 163 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.8292 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 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 118 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 20104 Z= 0.200 Angle : 0.777 13.321 27268 Z= 0.370 Chirality : 0.043 0.184 3092 Planarity : 0.004 0.055 3448 Dihedral : 7.746 133.463 2692 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.21 % Favored : 91.71 % Rotamer Outliers : 0.00 % 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: -2.67 (0.17), residues: 2436 helix: -1.08 (0.14), residues: 1204 sheet: -6.44 (0.10), residues: 56 loop : -2.26 (0.19), residues: 1176 *********************** 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 571 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 2.468 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: 0 outliers final: 0 residues processed: 571 average time/residue: 0.2757 time to fit residues: 248.4150 Evaluate side-chains 453 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.306 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2549 ------------------------------------------------------------------------------- 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: 2.9990 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 20104 Z= 0.218 Angle : 0.798 13.472 27268 Z= 0.380 Chirality : 0.044 0.185 3092 Planarity : 0.004 0.042 3448 Dihedral : 7.008 111.896 2692 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.33 % Favored : 91.50 % Rotamer Outliers : 0.00 % 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: -2.54 (0.17), residues: 2436 helix: -0.91 (0.14), residues: 1212 sheet: -6.45 (0.10), residues: 56 loop : -2.27 (0.19), residues: 1168 *********************** REFINEMENT MACRO_CYCLE 6 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 564 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.2802 time to fit residues: 250.4555 Evaluate side-chains 439 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 20104 Z= 0.229 Angle : 0.824 13.714 27268 Z= 0.389 Chirality : 0.045 0.193 3092 Planarity : 0.004 0.042 3448 Dihedral : 6.173 77.695 2692 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.58 % Favored : 91.30 % Rotamer Outliers : 0.00 % 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: -2.36 (0.17), residues: 2436 helix: -0.80 (0.14), residues: 1228 sheet: -6.46 (0.10), residues: 56 loop : -2.13 (0.19), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 7 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 531 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 2.574 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 outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.2656 time to fit residues: 225.4347 Evaluate side-chains 422 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 20104 Z= 0.212 Angle : 0.833 13.518 27268 Z= 0.390 Chirality : 0.044 0.186 3092 Planarity : 0.004 0.064 3448 Dihedral : 5.943 58.544 2692 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.25 % Favored : 91.63 % Rotamer Outliers : 0.05 % 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: -2.15 (0.17), residues: 2436 helix: -0.59 (0.15), residues: 1216 sheet: -6.49 (0.10), residues: 56 loop : -2.07 (0.19), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 8 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 536 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 2.343 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 outliers start: 1 outliers final: 0 residues processed: 536 average time/residue: 0.2685 time to fit residues: 230.9404 Evaluate side-chains 435 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 20104 Z= 0.214 Angle : 0.843 14.671 27268 Z= 0.393 Chirality : 0.045 0.199 3092 Planarity : 0.004 0.041 3448 Dihedral : 5.923 62.800 2692 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 0.00 % 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: -2.06 (0.17), residues: 2436 helix: -0.53 (0.15), residues: 1216 sheet: -6.49 (0.11), residues: 56 loop : -1.99 (0.19), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 9 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 537 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.2756 time to fit residues: 234.9687 Evaluate side-chains 432 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.4980 chunk 231 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 20104 Z= 0.235 Angle : 0.846 13.788 27268 Z= 0.400 Chirality : 0.045 0.176 3092 Planarity : 0.004 0.062 3448 Dihedral : 5.991 63.382 2692 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.87 % Favored : 91.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.97 (0.17), residues: 2436 helix: -0.48 (0.15), residues: 1216 sheet: -6.51 (0.10), residues: 56 loop : -1.93 (0.20), residues: 1164 ********************** REFINEMENT MACRO_CYCLE 10 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 531 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.2746 time to fit residues: 232.2459 Evaluate side-chains 422 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 178 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 199 optimal weight: 0.0030 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084103 restraints weight = 54521.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086507 restraints weight = 34748.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088241 restraints weight = 24950.654| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 20104 Z= 0.202 Angle : 0.850 14.644 27268 Z= 0.395 Chirality : 0.045 0.194 3092 Planarity : 0.004 0.041 3448 Dihedral : 5.921 66.060 2692 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.83 % Favored : 91.09 % Rotamer Outliers : 0.05 % 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: -1.96 (0.17), residues: 2436 helix: -0.39 (0.15), residues: 1204 sheet: -6.48 (0.10), residues: 56 loop : -2.02 (0.19), residues: 1176 =============================================================================== Job complete usr+sys time: 4618.83 seconds wall clock time: 84 minutes 13.54 seconds (5053.54 seconds total)