Starting phenix.real_space_refine on Sat Feb 17 19:10:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/02_2024/6d7t_7825_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/02_2024/6d7t_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_7825/02_2024/6d7t_7825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/02_2024/6d7t_7825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/02_2024/6d7t_7825_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7t_7825/02_2024/6d7t_7825_updated.pdb" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.87, per 1000 atoms: 0.50 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: 7.85 Conformation dependent library (CDL) restraints added in 3.2 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: 5.84 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: 7.82 Time building geometry restraints manager: 8.34 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: 11744 35.95 - 71.89: 268 71.89 - 107.84: 4 107.84 - 143.78: 0 143.78 - 179.73: 4 Dihedral angle restraints: 12020 sinusoidal: 4876 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 12017 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 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: 1.080 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: 2.950 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 56.860 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 14.784 179.729 7404 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 % Allowed : 9.12 % Favored : 85.40 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 613 HIS 0.027 0.004 HIS B 522 PHE 0.028 0.004 PHE C 434 TYR 0.029 0.004 TYR B 324 ARG 0.032 0.002 ARG C 153 *********************** 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 : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 VAL cc_start: 0.8814 (t) cc_final: 0.8340 (p) REVERT: A 127 ASN cc_start: 0.8740 (m110) cc_final: 0.8359 (p0) REVERT: A 208 ASN cc_start: 0.9184 (t160) cc_final: 0.8869 (t0) REVERT: A 211 PHE cc_start: 0.8369 (t80) cc_final: 0.7487 (t80) REVERT: A 229 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 280 LEU cc_start: 0.9115 (tp) cc_final: 0.8766 (tp) REVERT: A 324 TYR cc_start: 0.7964 (p90) cc_final: 0.7137 (p90) REVERT: A 364 ASP cc_start: 0.9212 (m-30) cc_final: 0.8838 (t0) REVERT: A 367 LEU cc_start: 0.8970 (tt) cc_final: 0.7577 (tt) REVERT: A 398 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9221 (tt) REVERT: A 435 MET cc_start: 0.9039 (mmp) cc_final: 0.8750 (mmm) REVERT: A 438 VAL cc_start: 0.9293 (p) cc_final: 0.9063 (m) REVERT: A 442 MET cc_start: 0.8924 (tpp) cc_final: 0.8428 (tpp) REVERT: A 462 TRP cc_start: 0.9423 (m100) cc_final: 0.9108 (m100) REVERT: A 464 ASN cc_start: 0.8909 (t160) cc_final: 0.8539 (t0) REVERT: A 497 MET cc_start: 0.8689 (tmm) cc_final: 0.8483 (tmm) REVERT: A 509 TYR cc_start: 0.9206 (t80) cc_final: 0.8449 (t80) REVERT: A 515 GLU cc_start: 0.8754 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 520 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8098 (tm) REVERT: A 577 MET cc_start: 0.8688 (mmm) cc_final: 0.8341 (mmm) REVERT: B 58 VAL cc_start: 0.8782 (t) cc_final: 0.8288 (p) REVERT: B 127 ASN cc_start: 0.8698 (m110) cc_final: 0.8402 (p0) REVERT: B 208 ASN cc_start: 0.9178 (t160) cc_final: 0.8857 (t0) REVERT: B 211 PHE cc_start: 0.8361 (t80) cc_final: 0.7487 (t80) REVERT: B 229 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 324 TYR cc_start: 0.7965 (p90) cc_final: 0.7138 (p90) REVERT: B 364 ASP cc_start: 0.9207 (m-30) cc_final: 0.8849 (t0) REVERT: B 398 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9231 (tt) REVERT: B 435 MET cc_start: 0.9039 (mmp) cc_final: 0.8784 (mmm) REVERT: B 438 VAL cc_start: 0.9289 (p) cc_final: 0.9059 (m) REVERT: B 442 MET cc_start: 0.8924 (tpp) cc_final: 0.8432 (tpp) REVERT: B 462 TRP cc_start: 0.9426 (m100) cc_final: 0.9081 (m100) REVERT: B 464 ASN cc_start: 0.8906 (t160) cc_final: 0.8391 (t0) REVERT: B 509 TYR cc_start: 0.9200 (t80) cc_final: 0.8431 (t80) REVERT: B 515 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7897 (mm-30) REVERT: B 528 MET cc_start: 0.8353 (ttm) cc_final: 0.8125 (ttm) REVERT: C 58 VAL cc_start: 0.8846 (t) cc_final: 0.8405 (p) REVERT: C 127 ASN cc_start: 0.8733 (m110) cc_final: 0.8386 (p0) REVERT: C 208 ASN cc_start: 0.9166 (t160) cc_final: 0.8851 (t0) REVERT: C 211 PHE cc_start: 0.8373 (t80) cc_final: 0.7423 (t80) REVERT: C 229 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7776 (mp) REVERT: C 245 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9068 (mttt) REVERT: C 280 LEU cc_start: 0.9117 (tp) cc_final: 0.8729 (tp) REVERT: C 324 TYR cc_start: 0.8043 (p90) cc_final: 0.7269 (p90) REVERT: C 364 ASP cc_start: 0.9207 (m-30) cc_final: 0.8646 (t70) REVERT: C 367 LEU cc_start: 0.8969 (tt) cc_final: 0.7589 (tt) REVERT: C 398 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9230 (tt) REVERT: C 435 MET cc_start: 0.9040 (mmp) cc_final: 0.8736 (mmm) REVERT: C 438 VAL cc_start: 0.9299 (p) cc_final: 0.9083 (m) REVERT: C 442 MET cc_start: 0.8928 (tpp) cc_final: 0.8436 (tpp) REVERT: C 462 TRP cc_start: 0.9392 (m100) cc_final: 0.9128 (m100) REVERT: C 464 ASN cc_start: 0.8924 (t160) cc_final: 0.8564 (t0) REVERT: C 497 MET cc_start: 0.8694 (tmm) cc_final: 0.8319 (tmm) REVERT: C 509 TYR cc_start: 0.9199 (t80) cc_final: 0.8384 (t80) REVERT: C 520 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8093 (tm) REVERT: C 528 MET cc_start: 0.8405 (ttm) cc_final: 0.8182 (ttm) REVERT: C 577 MET cc_start: 0.8720 (mmm) cc_final: 0.8409 (mmm) REVERT: D 58 VAL cc_start: 0.8814 (t) cc_final: 0.8362 (p) REVERT: D 127 ASN cc_start: 0.8705 (m110) cc_final: 0.8408 (p0) REVERT: D 208 ASN cc_start: 0.9166 (t160) cc_final: 0.8842 (t0) REVERT: D 211 PHE cc_start: 0.8358 (t80) cc_final: 0.7475 (t80) REVERT: D 229 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7784 (mp) REVERT: D 245 LYS cc_start: 0.9295 (ptpp) cc_final: 0.9093 (mttt) REVERT: D 280 LEU cc_start: 0.9113 (tp) cc_final: 0.8738 (tp) REVERT: D 324 TYR cc_start: 0.8034 (p90) cc_final: 0.7228 (p90) REVERT: D 364 ASP cc_start: 0.9219 (m-30) cc_final: 0.8639 (t70) REVERT: D 367 LEU cc_start: 0.8959 (tt) cc_final: 0.7619 (tt) REVERT: D 398 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9208 (tt) REVERT: D 435 MET cc_start: 0.9026 (mmp) cc_final: 0.8747 (mmm) REVERT: D 438 VAL cc_start: 0.9280 (p) cc_final: 0.9068 (m) REVERT: D 442 MET cc_start: 0.8950 (tpp) cc_final: 0.8428 (tpp) REVERT: D 462 TRP cc_start: 0.9413 (m100) cc_final: 0.9114 (m100) REVERT: D 464 ASN cc_start: 0.8906 (t160) cc_final: 0.8551 (t0) REVERT: D 485 MET cc_start: 0.8547 (mmt) cc_final: 0.8041 (mmt) REVERT: D 497 MET cc_start: 0.8721 (tmm) cc_final: 0.8405 (tmm) REVERT: D 509 TYR cc_start: 0.9221 (t80) cc_final: 0.8380 (t80) REVERT: D 515 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7927 (mm-30) REVERT: D 520 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8063 (tm) REVERT: D 528 MET cc_start: 0.8389 (ttm) cc_final: 0.8177 (ttm) REVERT: D 542 ASP cc_start: 0.8044 (t70) cc_final: 0.7690 (p0) REVERT: D 577 MET cc_start: 0.8716 (mmm) cc_final: 0.6940 (mmm) outliers start: 116 outliers final: 32 residues processed: 683 average time/residue: 0.3510 time to fit residues: 353.0020 Evaluate side-chains 499 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 456 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.0770 chunk 142 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 158 ASN ** 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 158 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 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 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: 0.8167 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20104 Z= 0.216 Angle : 0.832 13.048 27268 Z= 0.413 Chirality : 0.045 0.168 3092 Planarity : 0.005 0.048 3448 Dihedral : 9.721 171.668 2700 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.84 % Favored : 92.00 % Rotamer: Outliers : 0.43 % Allowed : 7.70 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.15), residues: 2436 helix: -2.54 (0.12), residues: 1264 sheet: -6.41 (0.10), residues: 56 loop : -2.81 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 583 HIS 0.006 0.001 HIS B 522 PHE 0.017 0.001 PHE D 504 TYR 0.019 0.002 TYR B 432 ARG 0.004 0.001 ARG C 606 *********************** 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: 9 poor density : 619 time to evaluate : 2.203 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: A 92 LEU cc_start: 0.8835 (pt) cc_final: 0.8564 (tt) REVERT: A 110 MET cc_start: 0.8995 (mmm) cc_final: 0.7904 (mmm) REVERT: A 127 ASN cc_start: 0.8723 (m110) cc_final: 0.8436 (p0) REVERT: A 204 ILE cc_start: 0.9613 (mm) cc_final: 0.9365 (mm) REVERT: A 209 LYS cc_start: 0.9710 (mtpt) cc_final: 0.9000 (mtpp) REVERT: A 211 PHE cc_start: 0.8351 (t80) cc_final: 0.7681 (t80) REVERT: A 303 GLU cc_start: 0.8390 (tp30) cc_final: 0.8161 (tp30) REVERT: A 306 GLN cc_start: 0.8895 (mp10) cc_final: 0.8522 (mp10) REVERT: A 318 SER cc_start: 0.9359 (t) cc_final: 0.8959 (t) REVERT: A 364 ASP cc_start: 0.9260 (m-30) cc_final: 0.8599 (t70) REVERT: A 435 MET cc_start: 0.9061 (mmp) cc_final: 0.8804 (mmm) REVERT: A 442 MET cc_start: 0.8806 (tpp) cc_final: 0.8359 (tpp) REVERT: A 497 MET cc_start: 0.8887 (tmm) cc_final: 0.8324 (tmm) REVERT: A 504 PHE cc_start: 0.9162 (m-80) cc_final: 0.8925 (m-80) REVERT: A 509 TYR cc_start: 0.9079 (t80) cc_final: 0.8433 (t80) REVERT: A 557 ILE cc_start: 0.8949 (pt) cc_final: 0.8699 (tt) REVERT: A 570 MET cc_start: 0.8175 (ppp) cc_final: 0.7893 (tmm) REVERT: A 577 MET cc_start: 0.8760 (mmm) cc_final: 0.8474 (mmm) REVERT: B 110 MET cc_start: 0.8994 (mmm) cc_final: 0.7975 (mmm) REVERT: B 127 ASN cc_start: 0.8708 (m110) cc_final: 0.8457 (p0) REVERT: B 204 ILE cc_start: 0.9603 (mm) cc_final: 0.9355 (mm) REVERT: B 209 LYS cc_start: 0.9702 (mtpt) cc_final: 0.8984 (mtpp) REVERT: B 211 PHE cc_start: 0.8356 (t80) cc_final: 0.7661 (t80) REVERT: B 306 GLN cc_start: 0.8887 (mp10) cc_final: 0.8524 (mp10) REVERT: B 318 SER cc_start: 0.9332 (t) cc_final: 0.8959 (t) REVERT: B 364 ASP cc_start: 0.9244 (m-30) cc_final: 0.8612 (t70) REVERT: B 435 MET cc_start: 0.9048 (mmp) cc_final: 0.8808 (mmm) REVERT: B 442 MET cc_start: 0.8793 (tpp) cc_final: 0.8320 (tpp) REVERT: B 504 PHE cc_start: 0.9163 (m-80) cc_final: 0.8912 (m-80) REVERT: B 509 TYR cc_start: 0.9083 (t80) cc_final: 0.8440 (t80) REVERT: B 528 MET cc_start: 0.8329 (ttm) cc_final: 0.7999 (ttm) REVERT: B 557 ILE cc_start: 0.8939 (pt) cc_final: 0.8682 (tt) REVERT: C 110 MET cc_start: 0.9022 (mmm) cc_final: 0.7916 (mmm) REVERT: C 127 ASN cc_start: 0.8724 (m110) cc_final: 0.8475 (p0) REVERT: C 204 ILE cc_start: 0.9633 (mm) cc_final: 0.9382 (mm) REVERT: C 209 LYS cc_start: 0.9691 (mtpt) cc_final: 0.9009 (mtpp) REVERT: C 211 PHE cc_start: 0.8333 (t80) cc_final: 0.7640 (t80) REVERT: C 303 GLU cc_start: 0.8439 (tp30) cc_final: 0.8234 (tp30) REVERT: C 306 GLN cc_start: 0.8841 (mp10) cc_final: 0.8440 (mp10) REVERT: C 318 SER cc_start: 0.9333 (t) cc_final: 0.9002 (t) REVERT: C 364 ASP cc_start: 0.9256 (m-30) cc_final: 0.8633 (t70) REVERT: C 435 MET cc_start: 0.9060 (mmp) cc_final: 0.8757 (mmm) REVERT: C 442 MET cc_start: 0.8766 (tpp) cc_final: 0.8321 (tpp) REVERT: C 497 MET cc_start: 0.8802 (tmm) cc_final: 0.8339 (tmm) REVERT: C 509 TYR cc_start: 0.9070 (t80) cc_final: 0.8369 (t80) REVERT: C 557 ILE cc_start: 0.8981 (pt) cc_final: 0.8718 (tt) REVERT: C 577 MET cc_start: 0.8768 (mmm) cc_final: 0.8520 (mmm) REVERT: D 110 MET cc_start: 0.8987 (mmm) cc_final: 0.7951 (mmm) REVERT: D 127 ASN cc_start: 0.8728 (m110) cc_final: 0.8454 (p0) REVERT: D 204 ILE cc_start: 0.9621 (mm) cc_final: 0.9374 (mm) REVERT: D 209 LYS cc_start: 0.9689 (mtpt) cc_final: 0.9008 (mtpp) REVERT: D 211 PHE cc_start: 0.8343 (t80) cc_final: 0.7642 (t80) REVERT: D 303 GLU cc_start: 0.8442 (tp30) cc_final: 0.8241 (tp30) REVERT: D 306 GLN cc_start: 0.8869 (mp10) cc_final: 0.8456 (mp10) REVERT: D 318 SER cc_start: 0.9336 (t) cc_final: 0.8923 (t) REVERT: D 364 ASP cc_start: 0.9271 (m-30) cc_final: 0.8624 (t70) REVERT: D 442 MET cc_start: 0.8742 (tpp) cc_final: 0.8309 (tpp) REVERT: D 497 MET cc_start: 0.8878 (tmm) cc_final: 0.8346 (tmm) REVERT: D 504 PHE cc_start: 0.9094 (m-80) cc_final: 0.8776 (m-10) REVERT: D 509 TYR cc_start: 0.9128 (t80) cc_final: 0.8425 (t80) REVERT: D 528 MET cc_start: 0.8219 (ttm) cc_final: 0.7957 (ttm) REVERT: D 547 TYR cc_start: 0.8096 (m-10) cc_final: 0.7882 (m-10) REVERT: D 553 PHE cc_start: 0.8030 (t80) cc_final: 0.7810 (t80) REVERT: D 557 ILE cc_start: 0.8928 (pt) cc_final: 0.8672 (tt) REVERT: D 570 MET cc_start: 0.8268 (ppp) cc_final: 0.8054 (tmm) REVERT: D 577 MET cc_start: 0.8672 (mmm) cc_final: 0.8314 (mmm) outliers start: 9 outliers final: 0 residues processed: 620 average time/residue: 0.2876 time to fit residues: 275.6751 Evaluate side-chains 468 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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: 7.9990 chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 0.3980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 596 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 158 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 596 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 158 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20104 Z= 0.221 Angle : 0.781 14.175 27268 Z= 0.385 Chirality : 0.044 0.178 3092 Planarity : 0.004 0.047 3448 Dihedral : 9.150 168.994 2700 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.09 % Favored : 91.75 % Rotamer: Outliers : 0.19 % Allowed : 6.05 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.16), residues: 2436 helix: -1.89 (0.13), residues: 1268 sheet: -6.41 (0.10), residues: 56 loop : -2.48 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 629 HIS 0.005 0.001 HIS A 265 PHE 0.018 0.002 PHE B 493 TYR 0.013 0.002 TYR B 216 ARG 0.006 0.000 ARG B 589 *********************** 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 573 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 569 time to evaluate : 2.032 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: A 92 LEU cc_start: 0.8946 (pt) cc_final: 0.8647 (tt) REVERT: A 110 MET cc_start: 0.8988 (mmm) cc_final: 0.7877 (mmm) REVERT: A 127 ASN cc_start: 0.8563 (m110) cc_final: 0.8192 (p0) REVERT: A 130 MET cc_start: 0.8324 (mmm) cc_final: 0.7872 (mmt) REVERT: A 200 LEU cc_start: 0.9604 (mt) cc_final: 0.9378 (mm) REVERT: A 209 LYS cc_start: 0.9714 (mtpt) cc_final: 0.9157 (mtpp) REVERT: A 211 PHE cc_start: 0.8257 (t80) cc_final: 0.7713 (t80) REVERT: A 303 GLU cc_start: 0.8505 (tp30) cc_final: 0.8144 (tp30) REVERT: A 306 GLN cc_start: 0.8950 (mp10) cc_final: 0.8396 (mp10) REVERT: A 318 SER cc_start: 0.9351 (t) cc_final: 0.8839 (p) REVERT: A 364 ASP cc_start: 0.9288 (m-30) cc_final: 0.8618 (t70) REVERT: A 399 ILE cc_start: 0.9602 (pt) cc_final: 0.8932 (tt) REVERT: A 442 MET cc_start: 0.8501 (tpp) cc_final: 0.8202 (tpp) REVERT: A 497 MET cc_start: 0.8924 (tmm) cc_final: 0.8318 (tmm) REVERT: A 509 TYR cc_start: 0.9052 (t80) cc_final: 0.8468 (t80) REVERT: A 557 ILE cc_start: 0.9182 (pt) cc_final: 0.8839 (tt) REVERT: A 577 MET cc_start: 0.8653 (mmm) cc_final: 0.8370 (mmm) REVERT: A 603 MET cc_start: 0.8173 (mmm) cc_final: 0.7708 (mtm) REVERT: A 612 LEU cc_start: 0.8719 (tt) cc_final: 0.8256 (mm) REVERT: B 92 LEU cc_start: 0.8830 (pt) cc_final: 0.8625 (tt) REVERT: B 110 MET cc_start: 0.9018 (mmm) cc_final: 0.7885 (mmm) REVERT: B 127 ASN cc_start: 0.8556 (m110) cc_final: 0.8262 (p0) REVERT: B 130 MET cc_start: 0.7917 (mmt) cc_final: 0.7495 (mmm) REVERT: B 204 ILE cc_start: 0.9639 (mm) cc_final: 0.9402 (mm) REVERT: B 209 LYS cc_start: 0.9712 (mtpt) cc_final: 0.9155 (mtpp) REVERT: B 211 PHE cc_start: 0.8269 (t80) cc_final: 0.7720 (t80) REVERT: B 303 GLU cc_start: 0.8438 (tp30) cc_final: 0.8028 (tp30) REVERT: B 306 GLN cc_start: 0.8856 (mp10) cc_final: 0.8368 (mp10) REVERT: B 318 SER cc_start: 0.9330 (t) cc_final: 0.9124 (t) REVERT: B 364 ASP cc_start: 0.9289 (m-30) cc_final: 0.8628 (t70) REVERT: B 399 ILE cc_start: 0.9592 (pt) cc_final: 0.9186 (pt) REVERT: B 442 MET cc_start: 0.8519 (tpp) cc_final: 0.8196 (tpp) REVERT: B 497 MET cc_start: 0.9266 (tmm) cc_final: 0.8951 (tmm) REVERT: B 509 TYR cc_start: 0.9055 (t80) cc_final: 0.8471 (t80) REVERT: B 528 MET cc_start: 0.8231 (ttm) cc_final: 0.7897 (ttm) REVERT: B 557 ILE cc_start: 0.9191 (pt) cc_final: 0.8848 (tt) REVERT: B 603 MET cc_start: 0.8176 (mmm) cc_final: 0.7717 (mtm) REVERT: B 627 ASP cc_start: 0.8858 (m-30) cc_final: 0.8628 (m-30) REVERT: B 629 TRP cc_start: 0.8075 (m-10) cc_final: 0.7788 (m-10) REVERT: C 92 LEU cc_start: 0.8869 (pt) cc_final: 0.8623 (tt) REVERT: C 110 MET cc_start: 0.8998 (mmm) cc_final: 0.7851 (mmm) REVERT: C 127 ASN cc_start: 0.8582 (m110) cc_final: 0.8294 (p0) REVERT: C 130 MET cc_start: 0.8121 (mmt) cc_final: 0.7636 (mmt) REVERT: C 209 LYS cc_start: 0.9713 (mtpt) cc_final: 0.9150 (mtpp) REVERT: C 211 PHE cc_start: 0.8247 (t80) cc_final: 0.7700 (t80) REVERT: C 318 SER cc_start: 0.9370 (t) cc_final: 0.8885 (p) REVERT: C 364 ASP cc_start: 0.9277 (m-30) cc_final: 0.8646 (t70) REVERT: C 399 ILE cc_start: 0.9613 (pt) cc_final: 0.9310 (tt) REVERT: C 442 MET cc_start: 0.8487 (tpp) cc_final: 0.8154 (tpp) REVERT: C 497 MET cc_start: 0.8841 (tmm) cc_final: 0.8364 (tmm) REVERT: C 509 TYR cc_start: 0.9049 (t80) cc_final: 0.8392 (t80) REVERT: C 557 ILE cc_start: 0.9223 (pt) cc_final: 0.8874 (tt) REVERT: C 577 MET cc_start: 0.8637 (mmm) cc_final: 0.8265 (mmm) REVERT: C 603 MET cc_start: 0.8208 (mmm) cc_final: 0.7916 (mtt) REVERT: C 627 ASP cc_start: 0.8868 (m-30) cc_final: 0.8628 (m-30) REVERT: C 629 TRP cc_start: 0.8156 (m-10) cc_final: 0.7916 (m-10) REVERT: D 92 LEU cc_start: 0.8950 (pt) cc_final: 0.8650 (tt) REVERT: D 110 MET cc_start: 0.8946 (mmm) cc_final: 0.7842 (mmm) REVERT: D 127 ASN cc_start: 0.8566 (m110) cc_final: 0.8162 (p0) REVERT: D 130 MET cc_start: 0.8371 (mmm) cc_final: 0.7891 (mmt) REVERT: D 209 LYS cc_start: 0.9712 (mtpt) cc_final: 0.9145 (mtpp) REVERT: D 211 PHE cc_start: 0.8241 (t80) cc_final: 0.7702 (t80) REVERT: D 303 GLU cc_start: 0.8503 (tp30) cc_final: 0.8120 (tp30) REVERT: D 306 GLN cc_start: 0.8924 (mp10) cc_final: 0.8350 (mp10) REVERT: D 318 SER cc_start: 0.9361 (t) cc_final: 0.8868 (p) REVERT: D 364 ASP cc_start: 0.9295 (m-30) cc_final: 0.8646 (t70) REVERT: D 399 ILE cc_start: 0.9609 (pt) cc_final: 0.8964 (tt) REVERT: D 435 MET cc_start: 0.8992 (mmm) cc_final: 0.8714 (mmm) REVERT: D 442 MET cc_start: 0.8490 (tpp) cc_final: 0.8182 (tpp) REVERT: D 497 MET cc_start: 0.8898 (tmm) cc_final: 0.8351 (tmm) REVERT: D 509 TYR cc_start: 0.9083 (t80) cc_final: 0.8392 (t80) REVERT: D 528 MET cc_start: 0.8144 (ttm) cc_final: 0.7859 (ttm) REVERT: D 554 MET cc_start: 0.8316 (mtp) cc_final: 0.8059 (mtp) REVERT: D 557 ILE cc_start: 0.9150 (pt) cc_final: 0.8850 (tt) REVERT: D 577 MET cc_start: 0.8322 (mmm) cc_final: 0.7386 (mmm) REVERT: D 603 MET cc_start: 0.8178 (mmm) cc_final: 0.7914 (mtt) REVERT: D 612 LEU cc_start: 0.8786 (tt) cc_final: 0.8344 (mm) outliers start: 4 outliers final: 0 residues processed: 569 average time/residue: 0.2679 time to fit residues: 241.2250 Evaluate side-chains 456 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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: 9.9990 chunk 166 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 0.0970 chunk 235 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 211 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 overall best weight: 1.3980 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20104 Z= 0.224 Angle : 0.777 14.657 27268 Z= 0.379 Chirality : 0.044 0.158 3092 Planarity : 0.004 0.049 3448 Dihedral : 8.782 163.556 2700 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.46 % Rotamer: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % 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: -3.06 (0.16), residues: 2436 helix: -1.51 (0.13), residues: 1232 sheet: -6.45 (0.09), residues: 56 loop : -2.34 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 583 HIS 0.009 0.001 HIS A 522 PHE 0.026 0.002 PHE B 504 TYR 0.013 0.001 TYR D 216 ARG 0.006 0.000 ARG A 589 *********************** 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 572 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 568 time to evaluate : 2.480 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: A 92 LEU cc_start: 0.8962 (pt) cc_final: 0.8574 (tt) REVERT: A 110 MET cc_start: 0.8974 (mmm) cc_final: 0.8121 (mmm) REVERT: A 127 ASN cc_start: 0.8476 (m110) cc_final: 0.8157 (p0) REVERT: A 130 MET cc_start: 0.8264 (mmm) cc_final: 0.7802 (mmt) REVERT: A 209 LYS cc_start: 0.9680 (mtpt) cc_final: 0.9224 (mtpp) REVERT: A 211 PHE cc_start: 0.8257 (t80) cc_final: 0.7719 (t80) REVERT: A 298 THR cc_start: 0.8922 (m) cc_final: 0.8699 (p) REVERT: A 306 GLN cc_start: 0.8947 (mp10) cc_final: 0.8280 (mp10) REVERT: A 318 SER cc_start: 0.9384 (t) cc_final: 0.8923 (p) REVERT: A 364 ASP cc_start: 0.9143 (m-30) cc_final: 0.8634 (t70) REVERT: A 497 MET cc_start: 0.8755 (tmm) cc_final: 0.8416 (tmm) REVERT: A 509 TYR cc_start: 0.9071 (t80) cc_final: 0.8404 (t80) REVERT: A 556 SER cc_start: 0.9213 (m) cc_final: 0.8858 (p) REVERT: A 557 ILE cc_start: 0.9214 (pt) cc_final: 0.8805 (tt) REVERT: A 570 MET cc_start: 0.8162 (ppp) cc_final: 0.7677 (tmm) REVERT: A 573 LEU cc_start: 0.9249 (tt) cc_final: 0.8988 (tt) REVERT: A 577 MET cc_start: 0.8644 (mmm) cc_final: 0.8297 (mmm) REVERT: A 584 ARG cc_start: 0.6309 (mmt180) cc_final: 0.5901 (mmt180) REVERT: A 603 MET cc_start: 0.8328 (mmm) cc_final: 0.8050 (mtt) REVERT: A 612 LEU cc_start: 0.8733 (tt) cc_final: 0.8311 (mm) REVERT: B 92 LEU cc_start: 0.8911 (pt) cc_final: 0.8534 (tt) REVERT: B 110 MET cc_start: 0.8954 (mmm) cc_final: 0.8071 (mmm) REVERT: B 127 ASN cc_start: 0.8475 (m110) cc_final: 0.8229 (p0) REVERT: B 130 MET cc_start: 0.8041 (mmt) cc_final: 0.7800 (mtt) REVERT: B 209 LYS cc_start: 0.9694 (mtpt) cc_final: 0.9234 (mtpp) REVERT: B 211 PHE cc_start: 0.8256 (t80) cc_final: 0.7715 (t80) REVERT: B 245 LYS cc_start: 0.9141 (mttt) cc_final: 0.8889 (mptt) REVERT: B 303 GLU cc_start: 0.8457 (tp30) cc_final: 0.8216 (tp30) REVERT: B 318 SER cc_start: 0.9365 (t) cc_final: 0.8916 (p) REVERT: B 364 ASP cc_start: 0.9145 (m-30) cc_final: 0.8638 (t70) REVERT: B 497 MET cc_start: 0.9178 (tmm) cc_final: 0.8584 (tmm) REVERT: B 509 TYR cc_start: 0.9070 (t80) cc_final: 0.8424 (t80) REVERT: B 528 MET cc_start: 0.8147 (ttm) cc_final: 0.7857 (ttm) REVERT: B 556 SER cc_start: 0.9226 (m) cc_final: 0.8833 (p) REVERT: B 557 ILE cc_start: 0.9242 (pt) cc_final: 0.8849 (tt) REVERT: B 578 MET cc_start: 0.8268 (tmm) cc_final: 0.7963 (tmm) REVERT: B 584 ARG cc_start: 0.6234 (mmt180) cc_final: 0.5950 (mmt180) REVERT: B 603 MET cc_start: 0.8344 (mmm) cc_final: 0.8036 (mtt) REVERT: B 612 LEU cc_start: 0.8724 (tt) cc_final: 0.8298 (mm) REVERT: C 44 ILE cc_start: 0.9372 (pt) cc_final: 0.9098 (pt) REVERT: C 92 LEU cc_start: 0.8919 (pt) cc_final: 0.8544 (tt) REVERT: C 96 MET cc_start: 0.8172 (ptt) cc_final: 0.7917 (ppp) REVERT: C 99 MET cc_start: 0.9041 (mmp) cc_final: 0.8834 (mmm) REVERT: C 110 MET cc_start: 0.8977 (mmm) cc_final: 0.8110 (mmm) REVERT: C 127 ASN cc_start: 0.8554 (m110) cc_final: 0.8280 (p0) REVERT: C 130 MET cc_start: 0.8040 (mmt) cc_final: 0.7780 (mtt) REVERT: C 209 LYS cc_start: 0.9694 (mtpt) cc_final: 0.9172 (mttp) REVERT: C 211 PHE cc_start: 0.8256 (t80) cc_final: 0.7697 (t80) REVERT: C 306 GLN cc_start: 0.8915 (mp10) cc_final: 0.8532 (mp10) REVERT: C 318 SER cc_start: 0.9386 (t) cc_final: 0.8910 (p) REVERT: C 364 ASP cc_start: 0.9142 (m-30) cc_final: 0.8654 (t70) REVERT: C 442 MET cc_start: 0.8487 (tpp) cc_final: 0.8003 (tpp) REVERT: C 485 MET cc_start: 0.8758 (mmt) cc_final: 0.8242 (mmt) REVERT: C 497 MET cc_start: 0.8701 (tmm) cc_final: 0.8398 (tmm) REVERT: C 509 TYR cc_start: 0.9055 (t80) cc_final: 0.8410 (t80) REVERT: C 556 SER cc_start: 0.9207 (m) cc_final: 0.8870 (p) REVERT: C 557 ILE cc_start: 0.9261 (pt) cc_final: 0.8893 (tt) REVERT: C 577 MET cc_start: 0.8675 (mmm) cc_final: 0.6945 (mmm) REVERT: C 584 ARG cc_start: 0.6473 (mmt180) cc_final: 0.6049 (mmt180) REVERT: C 603 MET cc_start: 0.8362 (mmm) cc_final: 0.8079 (mtt) REVERT: C 612 LEU cc_start: 0.8712 (tt) cc_final: 0.8306 (mm) REVERT: D 92 LEU cc_start: 0.8964 (pt) cc_final: 0.8584 (tt) REVERT: D 110 MET cc_start: 0.8917 (mmm) cc_final: 0.8044 (mmm) REVERT: D 127 ASN cc_start: 0.8533 (m110) cc_final: 0.8187 (p0) REVERT: D 130 MET cc_start: 0.8332 (mmm) cc_final: 0.7825 (mmt) REVERT: D 209 LYS cc_start: 0.9696 (mtpt) cc_final: 0.9227 (mttp) REVERT: D 211 PHE cc_start: 0.8228 (t80) cc_final: 0.7667 (t80) REVERT: D 318 SER cc_start: 0.9373 (t) cc_final: 0.8910 (p) REVERT: D 364 ASP cc_start: 0.9181 (m-30) cc_final: 0.8687 (t70) REVERT: D 435 MET cc_start: 0.8995 (mmm) cc_final: 0.8724 (mmm) REVERT: D 497 MET cc_start: 0.8819 (tmm) cc_final: 0.8439 (tmm) REVERT: D 509 TYR cc_start: 0.9084 (t80) cc_final: 0.8387 (t80) REVERT: D 528 MET cc_start: 0.8152 (ttm) cc_final: 0.7845 (ttm) REVERT: D 554 MET cc_start: 0.8414 (mtp) cc_final: 0.8166 (mtp) REVERT: D 557 ILE cc_start: 0.9184 (pt) cc_final: 0.8884 (tt) REVERT: D 570 MET cc_start: 0.8235 (ppp) cc_final: 0.8007 (tmm) REVERT: D 577 MET cc_start: 0.8421 (mmm) cc_final: 0.7484 (mmm) REVERT: D 584 ARG cc_start: 0.6315 (mmt180) cc_final: 0.6076 (mmt180) REVERT: D 603 MET cc_start: 0.8329 (mmm) cc_final: 0.8056 (mtt) REVERT: D 612 LEU cc_start: 0.8721 (tt) cc_final: 0.8326 (mm) outliers start: 4 outliers final: 0 residues processed: 568 average time/residue: 0.2887 time to fit residues: 255.6580 Evaluate side-chains 449 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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: 5.9990 chunk 133 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** 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 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 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 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: 0.8169 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20104 Z= 0.215 Angle : 0.779 15.066 27268 Z= 0.373 Chirality : 0.043 0.160 3092 Planarity : 0.004 0.060 3448 Dihedral : 8.349 155.170 2700 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % 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: -2.71 (0.16), residues: 2436 helix: -1.16 (0.14), residues: 1264 sheet: -6.44 (0.10), residues: 56 loop : -2.24 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 629 HIS 0.005 0.001 HIS A 522 PHE 0.036 0.002 PHE D 504 TYR 0.020 0.001 TYR C 67 ARG 0.013 0.001 ARG B 589 *********************** 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 569 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 2.206 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: A 92 LEU cc_start: 0.9090 (pt) cc_final: 0.8708 (tt) REVERT: A 99 MET cc_start: 0.8941 (mmp) cc_final: 0.8644 (mmm) REVERT: A 110 MET cc_start: 0.8887 (mmm) cc_final: 0.7948 (mmm) REVERT: A 127 ASN cc_start: 0.8411 (m-40) cc_final: 0.8130 (p0) REVERT: A 130 MET cc_start: 0.8421 (mmm) cc_final: 0.8026 (mmt) REVERT: A 209 LYS cc_start: 0.9674 (mtpt) cc_final: 0.9220 (mttp) REVERT: A 211 PHE cc_start: 0.8282 (t80) cc_final: 0.7738 (t80) REVERT: A 298 THR cc_start: 0.8944 (m) cc_final: 0.8710 (p) REVERT: A 318 SER cc_start: 0.9381 (t) cc_final: 0.8951 (p) REVERT: A 364 ASP cc_start: 0.9132 (m-30) cc_final: 0.8650 (t70) REVERT: A 432 TYR cc_start: 0.9177 (t80) cc_final: 0.8952 (t80) REVERT: A 442 MET cc_start: 0.8664 (tpp) cc_final: 0.8397 (tpp) REVERT: A 509 TYR cc_start: 0.9080 (t80) cc_final: 0.8422 (t80) REVERT: A 556 SER cc_start: 0.9174 (m) cc_final: 0.8824 (p) REVERT: A 557 ILE cc_start: 0.9220 (pt) cc_final: 0.8845 (tt) REVERT: A 570 MET cc_start: 0.8161 (ppp) cc_final: 0.7728 (tmm) REVERT: A 573 LEU cc_start: 0.9275 (tt) cc_final: 0.9036 (tt) REVERT: A 577 MET cc_start: 0.8553 (mmm) cc_final: 0.8117 (mmm) REVERT: A 584 ARG cc_start: 0.6264 (mmt180) cc_final: 0.6049 (mmt180) REVERT: A 612 LEU cc_start: 0.8784 (tt) cc_final: 0.8374 (mm) REVERT: B 57 ASP cc_start: 0.8386 (m-30) cc_final: 0.8159 (m-30) REVERT: B 92 LEU cc_start: 0.9016 (pt) cc_final: 0.8618 (tp) REVERT: B 110 MET cc_start: 0.8929 (mmm) cc_final: 0.8016 (mmm) REVERT: B 127 ASN cc_start: 0.8473 (m110) cc_final: 0.8151 (p0) REVERT: B 130 MET cc_start: 0.8140 (mmt) cc_final: 0.7913 (mmt) REVERT: B 209 LYS cc_start: 0.9683 (mtpt) cc_final: 0.9229 (mttp) REVERT: B 245 LYS cc_start: 0.9124 (mttt) cc_final: 0.8848 (mptt) REVERT: B 303 GLU cc_start: 0.8504 (tp30) cc_final: 0.8212 (tp30) REVERT: B 315 GLU cc_start: 0.8453 (tp30) cc_final: 0.8242 (tp30) REVERT: B 318 SER cc_start: 0.9364 (t) cc_final: 0.8935 (p) REVERT: B 364 ASP cc_start: 0.9135 (m-30) cc_final: 0.8664 (t70) REVERT: B 432 TYR cc_start: 0.9110 (t80) cc_final: 0.8791 (t80) REVERT: B 442 MET cc_start: 0.8668 (tpp) cc_final: 0.8387 (tpp) REVERT: B 497 MET cc_start: 0.9155 (tmm) cc_final: 0.8695 (tmm) REVERT: B 509 TYR cc_start: 0.9038 (t80) cc_final: 0.8377 (t80) REVERT: B 556 SER cc_start: 0.9240 (m) cc_final: 0.8831 (p) REVERT: B 557 ILE cc_start: 0.9243 (pt) cc_final: 0.8875 (tt) REVERT: B 578 MET cc_start: 0.8395 (tmm) cc_final: 0.8001 (tmm) REVERT: B 588 GLU cc_start: 0.7824 (mp0) cc_final: 0.7550 (mp0) REVERT: B 603 MET cc_start: 0.8275 (mmm) cc_final: 0.7861 (mtm) REVERT: B 612 LEU cc_start: 0.8728 (tt) cc_final: 0.8348 (mm) REVERT: C 44 ILE cc_start: 0.9313 (pt) cc_final: 0.9096 (pt) REVERT: C 92 LEU cc_start: 0.9021 (pt) cc_final: 0.8588 (tp) REVERT: C 110 MET cc_start: 0.8834 (mmm) cc_final: 0.7946 (mmm) REVERT: C 127 ASN cc_start: 0.8492 (m110) cc_final: 0.8179 (p0) REVERT: C 130 MET cc_start: 0.8156 (mmt) cc_final: 0.7953 (mmt) REVERT: C 209 LYS cc_start: 0.9684 (mtpt) cc_final: 0.9265 (mttt) REVERT: C 318 SER cc_start: 0.9374 (t) cc_final: 0.8949 (p) REVERT: C 364 ASP cc_start: 0.9121 (m-30) cc_final: 0.8658 (t70) REVERT: C 424 PRO cc_start: 0.8302 (Cg_endo) cc_final: 0.8047 (Cg_exo) REVERT: C 509 TYR cc_start: 0.9052 (t80) cc_final: 0.8358 (t80) REVERT: C 528 MET cc_start: 0.8450 (tpp) cc_final: 0.8210 (tpp) REVERT: C 556 SER cc_start: 0.9175 (m) cc_final: 0.8865 (p) REVERT: C 557 ILE cc_start: 0.9287 (pt) cc_final: 0.8897 (tt) REVERT: C 612 LEU cc_start: 0.8757 (tt) cc_final: 0.8413 (mm) REVERT: D 92 LEU cc_start: 0.9064 (pt) cc_final: 0.8691 (tt) REVERT: D 99 MET cc_start: 0.8951 (mmp) cc_final: 0.8648 (mmm) REVERT: D 110 MET cc_start: 0.8885 (mmm) cc_final: 0.7944 (mmm) REVERT: D 127 ASN cc_start: 0.8474 (m110) cc_final: 0.8221 (p0) REVERT: D 130 MET cc_start: 0.8331 (mmm) cc_final: 0.7872 (mmt) REVERT: D 209 LYS cc_start: 0.9677 (mtpt) cc_final: 0.9226 (mttp) REVERT: D 318 SER cc_start: 0.9374 (t) cc_final: 0.8937 (p) REVERT: D 364 ASP cc_start: 0.9146 (m-30) cc_final: 0.8744 (t70) REVERT: D 435 MET cc_start: 0.9134 (mmm) cc_final: 0.8798 (mmm) REVERT: D 442 MET cc_start: 0.8549 (tpp) cc_final: 0.8321 (tpp) REVERT: D 509 TYR cc_start: 0.9087 (t80) cc_final: 0.8393 (t80) REVERT: D 528 MET cc_start: 0.8193 (ttm) cc_final: 0.7851 (ttm) REVERT: D 554 MET cc_start: 0.8490 (mtp) cc_final: 0.8287 (mtm) REVERT: D 556 SER cc_start: 0.9209 (m) cc_final: 0.8808 (p) REVERT: D 557 ILE cc_start: 0.9201 (pt) cc_final: 0.8872 (tt) REVERT: D 612 LEU cc_start: 0.8788 (tt) cc_final: 0.8373 (mm) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.2823 time to fit residues: 251.2877 Evaluate side-chains 456 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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: 9.9990 chunk 212 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.2980 chunk 123 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** 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 127 ASN ** 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: 0.8130 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20104 Z= 0.190 Angle : 0.788 15.398 27268 Z= 0.370 Chirality : 0.043 0.184 3092 Planarity : 0.004 0.040 3448 Dihedral : 7.739 137.870 2700 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.00 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -2.47 (0.17), residues: 2436 helix: -0.86 (0.14), residues: 1224 sheet: -6.48 (0.10), residues: 56 loop : -2.25 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 462 HIS 0.010 0.001 HIS C 522 PHE 0.020 0.001 PHE D 493 TYR 0.021 0.001 TYR B 67 ARG 0.008 0.000 ARG C 589 *********************** 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 563 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 2.334 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: A 99 MET cc_start: 0.8919 (mmp) cc_final: 0.8623 (mmm) REVERT: A 110 MET cc_start: 0.8924 (mmm) cc_final: 0.8145 (mmm) REVERT: A 209 LYS cc_start: 0.9658 (mtpt) cc_final: 0.9177 (mttp) REVERT: A 298 THR cc_start: 0.9002 (m) cc_final: 0.8746 (p) REVERT: A 318 SER cc_start: 0.9369 (t) cc_final: 0.8941 (p) REVERT: A 364 ASP cc_start: 0.9134 (m-30) cc_final: 0.8747 (t70) REVERT: A 367 LEU cc_start: 0.8729 (tt) cc_final: 0.7085 (tt) REVERT: A 424 PRO cc_start: 0.8251 (Cg_endo) cc_final: 0.8034 (Cg_exo) REVERT: A 509 TYR cc_start: 0.9026 (t80) cc_final: 0.8339 (t80) REVERT: A 556 SER cc_start: 0.9120 (m) cc_final: 0.8807 (p) REVERT: A 557 ILE cc_start: 0.9226 (pt) cc_final: 0.8872 (tt) REVERT: A 568 LEU cc_start: 0.9341 (tp) cc_final: 0.8970 (mm) REVERT: A 600 THR cc_start: 0.9480 (m) cc_final: 0.9256 (p) REVERT: A 612 LEU cc_start: 0.8682 (tt) cc_final: 0.8365 (mm) REVERT: B 51 LEU cc_start: 0.9376 (tt) cc_final: 0.9078 (mt) REVERT: B 92 LEU cc_start: 0.8980 (pt) cc_final: 0.8504 (tp) REVERT: B 99 MET cc_start: 0.8945 (mmp) cc_final: 0.8601 (mmm) REVERT: B 110 MET cc_start: 0.8917 (mmm) cc_final: 0.7954 (mmm) REVERT: B 127 ASN cc_start: 0.8441 (m-40) cc_final: 0.8198 (p0) REVERT: B 209 LYS cc_start: 0.9667 (mtpt) cc_final: 0.9183 (mttp) REVERT: B 245 LYS cc_start: 0.9107 (mttt) cc_final: 0.8882 (mptt) REVERT: B 303 GLU cc_start: 0.8609 (tp30) cc_final: 0.8307 (tp30) REVERT: B 318 SER cc_start: 0.9356 (t) cc_final: 0.8924 (p) REVERT: B 364 ASP cc_start: 0.9142 (m-30) cc_final: 0.8753 (t70) REVERT: B 367 LEU cc_start: 0.8746 (tt) cc_final: 0.7137 (tt) REVERT: B 497 MET cc_start: 0.9069 (tmm) cc_final: 0.8508 (tmm) REVERT: B 509 TYR cc_start: 0.9035 (t80) cc_final: 0.8379 (t80) REVERT: B 515 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 534 PHE cc_start: 0.9528 (t80) cc_final: 0.9282 (t80) REVERT: B 556 SER cc_start: 0.9157 (m) cc_final: 0.8755 (p) REVERT: B 557 ILE cc_start: 0.9264 (pt) cc_final: 0.8956 (tt) REVERT: B 612 LEU cc_start: 0.8682 (tt) cc_final: 0.8383 (mm) REVERT: C 44 ILE cc_start: 0.9285 (pt) cc_final: 0.9065 (pt) REVERT: C 92 LEU cc_start: 0.8975 (pt) cc_final: 0.8559 (tp) REVERT: C 99 MET cc_start: 0.9008 (mmp) cc_final: 0.8600 (mmm) REVERT: C 110 MET cc_start: 0.8865 (mmm) cc_final: 0.8297 (mmm) REVERT: C 127 ASN cc_start: 0.8447 (m-40) cc_final: 0.8199 (p0) REVERT: C 209 LYS cc_start: 0.9628 (mtpt) cc_final: 0.9182 (mttp) REVERT: C 318 SER cc_start: 0.9376 (t) cc_final: 0.9013 (p) REVERT: C 364 ASP cc_start: 0.9134 (m-30) cc_final: 0.8767 (t70) REVERT: C 497 MET cc_start: 0.9029 (tmm) cc_final: 0.8627 (tmm) REVERT: C 509 TYR cc_start: 0.9053 (t80) cc_final: 0.8378 (t80) REVERT: C 515 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 528 MET cc_start: 0.8471 (tpp) cc_final: 0.8084 (tpp) REVERT: C 556 SER cc_start: 0.9203 (m) cc_final: 0.8817 (p) REVERT: C 557 ILE cc_start: 0.9276 (pt) cc_final: 0.8959 (tt) REVERT: C 600 THR cc_start: 0.9505 (m) cc_final: 0.9301 (p) REVERT: C 612 LEU cc_start: 0.8685 (tt) cc_final: 0.8440 (mm) REVERT: D 99 MET cc_start: 0.8922 (mmp) cc_final: 0.8611 (mmm) REVERT: D 110 MET cc_start: 0.8900 (mmm) cc_final: 0.8139 (mmm) REVERT: D 127 ASN cc_start: 0.8419 (m-40) cc_final: 0.8142 (p0) REVERT: D 209 LYS cc_start: 0.9647 (mtpt) cc_final: 0.9181 (mttp) REVERT: D 211 PHE cc_start: 0.8205 (t80) cc_final: 0.7834 (t80) REVERT: D 318 SER cc_start: 0.9411 (t) cc_final: 0.9019 (p) REVERT: D 364 ASP cc_start: 0.9126 (m-30) cc_final: 0.8760 (t70) REVERT: D 435 MET cc_start: 0.9132 (mmm) cc_final: 0.8810 (mmm) REVERT: D 509 TYR cc_start: 0.9030 (t80) cc_final: 0.8379 (t80) REVERT: D 554 MET cc_start: 0.8340 (mtp) cc_final: 0.8106 (mtm) REVERT: D 556 SER cc_start: 0.9146 (m) cc_final: 0.8753 (p) REVERT: D 557 ILE cc_start: 0.9191 (pt) cc_final: 0.8869 (tt) REVERT: D 570 MET cc_start: 0.8058 (ppp) cc_final: 0.7850 (tmm) REVERT: D 600 THR cc_start: 0.9531 (m) cc_final: 0.9315 (p) REVERT: D 612 LEU cc_start: 0.8681 (tt) cc_final: 0.8405 (mm) outliers start: 0 outliers final: 0 residues processed: 563 average time/residue: 0.2806 time to fit residues: 248.4598 Evaluate side-chains 457 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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: 8.9990 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 198 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 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 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 40 GLN ** 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20104 Z= 0.242 Angle : 0.790 13.338 27268 Z= 0.380 Chirality : 0.045 0.191 3092 Planarity : 0.004 0.033 3448 Dihedral : 7.311 124.795 2700 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.83 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: -2.28 (0.17), residues: 2436 helix: -0.68 (0.14), residues: 1244 sheet: -6.51 (0.10), residues: 56 loop : -2.19 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 583 HIS 0.006 0.001 HIS C 522 PHE 0.021 0.002 PHE B 493 TYR 0.017 0.001 TYR C 432 ARG 0.006 0.000 ARG A 589 *********************** 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 526 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 2.464 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: A 110 MET cc_start: 0.8844 (mmm) cc_final: 0.8049 (mmm) REVERT: A 209 LYS cc_start: 0.9631 (mtpt) cc_final: 0.9290 (mttt) REVERT: A 298 THR cc_start: 0.9028 (m) cc_final: 0.8772 (p) REVERT: A 315 GLU cc_start: 0.8619 (tp30) cc_final: 0.8344 (tp30) REVERT: A 318 SER cc_start: 0.9381 (t) cc_final: 0.8953 (p) REVERT: A 364 ASP cc_start: 0.9113 (m-30) cc_final: 0.8794 (t70) REVERT: A 367 LEU cc_start: 0.8733 (tt) cc_final: 0.7175 (tt) REVERT: A 424 PRO cc_start: 0.8328 (Cg_endo) cc_final: 0.8080 (Cg_exo) REVERT: A 509 TYR cc_start: 0.9020 (t80) cc_final: 0.8369 (t80) REVERT: A 515 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 556 SER cc_start: 0.9260 (m) cc_final: 0.8840 (p) REVERT: A 557 ILE cc_start: 0.9212 (pt) cc_final: 0.8892 (tt) REVERT: A 570 MET cc_start: 0.8320 (ppp) cc_final: 0.7970 (tmm) REVERT: A 600 THR cc_start: 0.9534 (m) cc_final: 0.9311 (p) REVERT: A 612 LEU cc_start: 0.8757 (tt) cc_final: 0.8487 (mm) REVERT: B 51 LEU cc_start: 0.9408 (tt) cc_final: 0.9107 (mt) REVERT: B 92 LEU cc_start: 0.9019 (pt) cc_final: 0.8653 (tp) REVERT: B 110 MET cc_start: 0.8829 (mmm) cc_final: 0.7949 (mmm) REVERT: B 209 LYS cc_start: 0.9619 (mtpt) cc_final: 0.9275 (mttt) REVERT: B 211 PHE cc_start: 0.8201 (t80) cc_final: 0.7708 (t80) REVERT: B 245 LYS cc_start: 0.9171 (mttt) cc_final: 0.8940 (mptt) REVERT: B 298 THR cc_start: 0.9047 (m) cc_final: 0.8745 (p) REVERT: B 303 GLU cc_start: 0.8705 (tp30) cc_final: 0.8418 (tp30) REVERT: B 315 GLU cc_start: 0.8637 (tp30) cc_final: 0.8334 (tp30) REVERT: B 318 SER cc_start: 0.9385 (t) cc_final: 0.8942 (p) REVERT: B 364 ASP cc_start: 0.9127 (m-30) cc_final: 0.8802 (t70) REVERT: B 367 LEU cc_start: 0.8749 (tt) cc_final: 0.7098 (tt) REVERT: B 497 MET cc_start: 0.9101 (tmm) cc_final: 0.8577 (tmm) REVERT: B 509 TYR cc_start: 0.9066 (t80) cc_final: 0.8423 (t80) REVERT: B 515 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7869 (mm-30) REVERT: B 528 MET cc_start: 0.8371 (tpp) cc_final: 0.8155 (tpp) REVERT: B 556 SER cc_start: 0.9276 (m) cc_final: 0.8869 (p) REVERT: B 557 ILE cc_start: 0.9273 (pt) cc_final: 0.8927 (tt) REVERT: B 612 LEU cc_start: 0.8748 (tt) cc_final: 0.8483 (mm) REVERT: C 92 LEU cc_start: 0.9020 (pt) cc_final: 0.8654 (tp) REVERT: C 110 MET cc_start: 0.8885 (mmm) cc_final: 0.8335 (mmm) REVERT: C 209 LYS cc_start: 0.9632 (mtpt) cc_final: 0.9280 (mttt) REVERT: C 211 PHE cc_start: 0.8162 (t80) cc_final: 0.7660 (t80) REVERT: C 280 LEU cc_start: 0.9134 (tp) cc_final: 0.8847 (tp) REVERT: C 298 THR cc_start: 0.8983 (m) cc_final: 0.8760 (p) REVERT: C 318 SER cc_start: 0.9402 (t) cc_final: 0.8987 (p) REVERT: C 364 ASP cc_start: 0.9106 (m-30) cc_final: 0.8810 (t70) REVERT: C 367 LEU cc_start: 0.8739 (tt) cc_final: 0.7134 (tt) REVERT: C 378 MET cc_start: 0.7512 (mmt) cc_final: 0.7310 (mmp) REVERT: C 410 MET cc_start: 0.5308 (tmm) cc_final: 0.5075 (ttp) REVERT: C 454 MET cc_start: 0.8666 (tpt) cc_final: 0.8243 (tpp) REVERT: C 509 TYR cc_start: 0.9045 (t80) cc_final: 0.8395 (t80) REVERT: C 515 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 528 MET cc_start: 0.8563 (tpp) cc_final: 0.8149 (tpp) REVERT: C 556 SER cc_start: 0.9295 (m) cc_final: 0.8869 (p) REVERT: C 557 ILE cc_start: 0.9272 (pt) cc_final: 0.8956 (tt) REVERT: C 600 THR cc_start: 0.9542 (m) cc_final: 0.9319 (p) REVERT: C 612 LEU cc_start: 0.8721 (tt) cc_final: 0.8500 (mm) REVERT: D 110 MET cc_start: 0.8879 (mmm) cc_final: 0.8095 (mmm) REVERT: D 209 LYS cc_start: 0.9631 (mtpt) cc_final: 0.9274 (mttt) REVERT: D 211 PHE cc_start: 0.8280 (t80) cc_final: 0.7697 (t80) REVERT: D 280 LEU cc_start: 0.9073 (tp) cc_final: 0.8788 (tp) REVERT: D 315 GLU cc_start: 0.8616 (tp30) cc_final: 0.8400 (tp30) REVERT: D 318 SER cc_start: 0.9393 (t) cc_final: 0.8961 (p) REVERT: D 364 ASP cc_start: 0.9126 (m-30) cc_final: 0.8804 (t70) REVERT: D 367 LEU cc_start: 0.8724 (tt) cc_final: 0.6952 (tt) REVERT: D 435 MET cc_start: 0.9150 (mmm) cc_final: 0.8843 (mmm) REVERT: D 509 TYR cc_start: 0.9065 (t80) cc_final: 0.8443 (t80) REVERT: D 515 GLU cc_start: 0.8683 (mm-30) cc_final: 0.7850 (mm-30) REVERT: D 528 MET cc_start: 0.8289 (tpp) cc_final: 0.8079 (tpp) REVERT: D 556 SER cc_start: 0.9243 (m) cc_final: 0.8874 (p) REVERT: D 600 THR cc_start: 0.9561 (m) cc_final: 0.9338 (p) REVERT: D 612 LEU cc_start: 0.8762 (tt) cc_final: 0.8471 (mm) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.2846 time to fit residues: 233.5667 Evaluate side-chains 452 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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: 0.3980 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.0030 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 0.0770 chunk 116 optimal weight: 8.9990 chunk 21 optimal weight: 0.0970 chunk 184 optimal weight: 5.9990 overall best weight: 0.1158 ------------------------------------------------------------------------------- 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 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 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20104 Z= 0.191 Angle : 0.835 13.718 27268 Z= 0.382 Chirality : 0.044 0.171 3092 Planarity : 0.004 0.031 3448 Dihedral : 6.343 77.944 2700 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: -0.52 (0.15), residues: 1216 sheet: -6.53 (0.10), residues: 56 loop : -2.15 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 268 HIS 0.003 0.001 HIS C 522 PHE 0.035 0.002 PHE D 504 TYR 0.019 0.001 TYR A 432 ARG 0.009 0.000 ARG B 589 *********************** 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 568 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 2.112 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: A 110 MET cc_start: 0.8866 (mmm) cc_final: 0.7926 (mmm) REVERT: A 127 ASN cc_start: 0.8506 (m-40) cc_final: 0.8196 (p0) REVERT: A 209 LYS cc_start: 0.9622 (mtpt) cc_final: 0.9202 (mttp) REVERT: A 211 PHE cc_start: 0.8165 (t80) cc_final: 0.7710 (t80) REVERT: A 298 THR cc_start: 0.8994 (m) cc_final: 0.8749 (p) REVERT: A 315 GLU cc_start: 0.8573 (tp30) cc_final: 0.8356 (tp30) REVERT: A 318 SER cc_start: 0.9356 (t) cc_final: 0.9007 (p) REVERT: A 364 ASP cc_start: 0.8999 (m-30) cc_final: 0.8737 (t70) REVERT: A 367 LEU cc_start: 0.8784 (tt) cc_final: 0.7125 (tt) REVERT: A 378 MET cc_start: 0.7409 (mmt) cc_final: 0.7193 (mmp) REVERT: A 509 TYR cc_start: 0.8889 (t80) cc_final: 0.8425 (t80) REVERT: A 515 GLU cc_start: 0.8695 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 528 MET cc_start: 0.8495 (tpp) cc_final: 0.8007 (tpp) REVERT: A 556 SER cc_start: 0.9151 (m) cc_final: 0.8651 (p) REVERT: A 557 ILE cc_start: 0.9135 (pt) cc_final: 0.8781 (tt) REVERT: A 568 LEU cc_start: 0.9253 (tp) cc_final: 0.8986 (mm) REVERT: A 570 MET cc_start: 0.8172 (ppp) cc_final: 0.7830 (tmm) REVERT: B 92 LEU cc_start: 0.8869 (pt) cc_final: 0.8485 (tp) REVERT: B 110 MET cc_start: 0.8806 (mmm) cc_final: 0.7789 (mmm) REVERT: B 209 LYS cc_start: 0.9622 (mtpt) cc_final: 0.9204 (mttp) REVERT: B 211 PHE cc_start: 0.8148 (t80) cc_final: 0.7661 (t80) REVERT: B 298 THR cc_start: 0.8977 (m) cc_final: 0.8715 (p) REVERT: B 303 GLU cc_start: 0.8697 (tp30) cc_final: 0.8383 (tp30) REVERT: B 318 SER cc_start: 0.9351 (t) cc_final: 0.9028 (p) REVERT: B 364 ASP cc_start: 0.9030 (m-30) cc_final: 0.8741 (t70) REVERT: B 367 LEU cc_start: 0.8798 (tt) cc_final: 0.7127 (tt) REVERT: B 378 MET cc_start: 0.7438 (mmt) cc_final: 0.7225 (mmp) REVERT: B 410 MET cc_start: 0.5308 (tmm) cc_final: 0.5054 (ttp) REVERT: B 497 MET cc_start: 0.8910 (tmm) cc_final: 0.8441 (tmm) REVERT: B 509 TYR cc_start: 0.8975 (t80) cc_final: 0.8400 (t80) REVERT: B 515 GLU cc_start: 0.8716 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 556 SER cc_start: 0.9140 (m) cc_final: 0.8782 (p) REVERT: B 557 ILE cc_start: 0.9236 (pt) cc_final: 0.8973 (tt) REVERT: C 92 LEU cc_start: 0.8864 (pt) cc_final: 0.8474 (tp) REVERT: C 110 MET cc_start: 0.8802 (mmm) cc_final: 0.8127 (mmm) REVERT: C 209 LYS cc_start: 0.9626 (mtpt) cc_final: 0.9226 (mttp) REVERT: C 211 PHE cc_start: 0.8163 (t80) cc_final: 0.7655 (t80) REVERT: C 280 LEU cc_start: 0.9130 (tp) cc_final: 0.8817 (tp) REVERT: C 298 THR cc_start: 0.9008 (m) cc_final: 0.8770 (p) REVERT: C 318 SER cc_start: 0.9378 (t) cc_final: 0.9042 (p) REVERT: C 367 LEU cc_start: 0.8791 (tt) cc_final: 0.7119 (tt) REVERT: C 378 MET cc_start: 0.7457 (mmt) cc_final: 0.7256 (mmp) REVERT: C 410 MET cc_start: 0.5200 (tmm) cc_final: 0.4873 (ttp) REVERT: C 432 TYR cc_start: 0.9151 (t80) cc_final: 0.8933 (t80) REVERT: C 454 MET cc_start: 0.8543 (tpt) cc_final: 0.7899 (tpt) REVERT: C 509 TYR cc_start: 0.8994 (t80) cc_final: 0.8395 (t80) REVERT: C 515 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7843 (mm-30) REVERT: C 528 MET cc_start: 0.8508 (tpp) cc_final: 0.8185 (tpp) REVERT: C 556 SER cc_start: 0.9161 (m) cc_final: 0.8697 (p) REVERT: C 557 ILE cc_start: 0.9210 (pt) cc_final: 0.8894 (tt) REVERT: D 110 MET cc_start: 0.8810 (mmm) cc_final: 0.7896 (mmm) REVERT: D 209 LYS cc_start: 0.9619 (mtpt) cc_final: 0.9210 (mttp) REVERT: D 211 PHE cc_start: 0.8260 (t80) cc_final: 0.7664 (t80) REVERT: D 250 GLU cc_start: 0.8475 (tp30) cc_final: 0.8260 (mm-30) REVERT: D 280 LEU cc_start: 0.9114 (tp) cc_final: 0.8791 (tp) REVERT: D 315 GLU cc_start: 0.8560 (tp30) cc_final: 0.8355 (tp30) REVERT: D 318 SER cc_start: 0.9367 (t) cc_final: 0.9010 (p) REVERT: D 367 LEU cc_start: 0.8802 (tt) cc_final: 0.7094 (tt) REVERT: D 435 MET cc_start: 0.9144 (mmm) cc_final: 0.8814 (mmm) REVERT: D 509 TYR cc_start: 0.8990 (t80) cc_final: 0.8393 (t80) REVERT: D 515 GLU cc_start: 0.8739 (mm-30) cc_final: 0.7869 (mm-30) REVERT: D 556 SER cc_start: 0.9078 (m) cc_final: 0.8692 (p) REVERT: D 557 ILE cc_start: 0.9150 (pt) cc_final: 0.8881 (tt) REVERT: D 613 TRP cc_start: 0.8136 (t60) cc_final: 0.7933 (t60) outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.2775 time to fit residues: 251.5199 Evaluate side-chains 441 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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: 2.9990 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 218 optimal weight: 0.0770 overall best weight: 2.1744 ------------------------------------------------------------------------------- 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 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 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 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20104 Z= 0.272 Angle : 0.836 13.616 27268 Z= 0.399 Chirality : 0.046 0.173 3092 Planarity : 0.004 0.054 3448 Dihedral : 5.894 52.050 2700 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.07 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2436 helix: -0.49 (0.15), residues: 1208 sheet: -6.58 (0.10), residues: 56 loop : -2.10 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 613 HIS 0.005 0.001 HIS C 522 PHE 0.035 0.002 PHE B 504 TYR 0.014 0.002 TYR C 432 ARG 0.007 0.000 ARG B 589 *********************** 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 524 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 2.491 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: A 110 MET cc_start: 0.8851 (mmm) cc_final: 0.7901 (mmm) REVERT: A 209 LYS cc_start: 0.9617 (mtpt) cc_final: 0.9246 (mttp) REVERT: A 211 PHE cc_start: 0.8218 (t80) cc_final: 0.7752 (t80) REVERT: A 298 THR cc_start: 0.9057 (m) cc_final: 0.8789 (p) REVERT: A 315 GLU cc_start: 0.8636 (tp30) cc_final: 0.8416 (tp30) REVERT: A 318 SER cc_start: 0.9360 (t) cc_final: 0.9002 (p) REVERT: A 364 ASP cc_start: 0.9045 (m-30) cc_final: 0.8837 (t70) REVERT: A 509 TYR cc_start: 0.9008 (t80) cc_final: 0.8470 (t80) REVERT: A 515 GLU cc_start: 0.8749 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 528 MET cc_start: 0.8660 (tpp) cc_final: 0.8160 (tpp) REVERT: A 556 SER cc_start: 0.9303 (m) cc_final: 0.8860 (p) REVERT: A 568 LEU cc_start: 0.9320 (tp) cc_final: 0.8986 (mm) REVERT: A 570 MET cc_start: 0.8309 (ppp) cc_final: 0.7995 (tmm) REVERT: B 92 LEU cc_start: 0.8802 (pt) cc_final: 0.8470 (tp) REVERT: B 99 MET cc_start: 0.9068 (mmp) cc_final: 0.8698 (mmp) REVERT: B 110 MET cc_start: 0.8802 (mmm) cc_final: 0.7787 (mmm) REVERT: B 209 LYS cc_start: 0.9615 (mtpt) cc_final: 0.9257 (mttp) REVERT: B 298 THR cc_start: 0.9061 (m) cc_final: 0.8815 (p) REVERT: B 315 GLU cc_start: 0.8681 (tp30) cc_final: 0.8438 (tp30) REVERT: B 318 SER cc_start: 0.9356 (t) cc_final: 0.9012 (p) REVERT: B 364 ASP cc_start: 0.9059 (m-30) cc_final: 0.8838 (t70) REVERT: B 497 MET cc_start: 0.9035 (tmm) cc_final: 0.8490 (tmm) REVERT: B 509 TYR cc_start: 0.8988 (t80) cc_final: 0.8400 (t80) REVERT: B 528 MET cc_start: 0.8500 (tpp) cc_final: 0.8214 (tpp) REVERT: B 556 SER cc_start: 0.9262 (m) cc_final: 0.8906 (p) REVERT: C 92 LEU cc_start: 0.8801 (pt) cc_final: 0.8446 (tp) REVERT: C 110 MET cc_start: 0.8904 (mmm) cc_final: 0.8284 (mmm) REVERT: C 209 LYS cc_start: 0.9626 (mtpt) cc_final: 0.9331 (mttt) REVERT: C 211 PHE cc_start: 0.8239 (t80) cc_final: 0.7753 (t80) REVERT: C 280 LEU cc_start: 0.9169 (tp) cc_final: 0.8902 (tp) REVERT: C 298 THR cc_start: 0.9046 (m) cc_final: 0.8819 (p) REVERT: C 318 SER cc_start: 0.9381 (t) cc_final: 0.9030 (p) REVERT: C 367 LEU cc_start: 0.8777 (tt) cc_final: 0.7113 (tt) REVERT: C 509 TYR cc_start: 0.9086 (t80) cc_final: 0.8444 (t80) REVERT: C 528 MET cc_start: 0.8620 (tpp) cc_final: 0.8117 (tpp) REVERT: C 556 SER cc_start: 0.9222 (m) cc_final: 0.8822 (p) REVERT: D 99 MET cc_start: 0.9092 (mmp) cc_final: 0.8768 (mmp) REVERT: D 110 MET cc_start: 0.8847 (mmm) cc_final: 0.7907 (mmm) REVERT: D 209 LYS cc_start: 0.9630 (mtpt) cc_final: 0.9260 (mttp) REVERT: D 211 PHE cc_start: 0.8381 (t80) cc_final: 0.7730 (t80) REVERT: D 280 LEU cc_start: 0.9165 (tp) cc_final: 0.8878 (tp) REVERT: D 318 SER cc_start: 0.9383 (t) cc_final: 0.9016 (p) REVERT: D 367 LEU cc_start: 0.8789 (tt) cc_final: 0.7103 (tt) REVERT: D 435 MET cc_start: 0.9138 (mmm) cc_final: 0.8852 (mmm) REVERT: D 480 ILE cc_start: 0.9287 (mm) cc_final: 0.9069 (mm) REVERT: D 509 TYR cc_start: 0.9071 (t80) cc_final: 0.8512 (t80) REVERT: D 515 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7817 (mm-30) REVERT: D 528 MET cc_start: 0.8519 (tpp) cc_final: 0.8252 (tpp) REVERT: D 556 SER cc_start: 0.9211 (m) cc_final: 0.8845 (p) REVERT: D 600 THR cc_start: 0.9533 (m) cc_final: 0.9314 (p) REVERT: D 613 TRP cc_start: 0.8110 (t60) cc_final: 0.7880 (t60) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.2785 time to fit residues: 232.1132 Evaluate side-chains 439 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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: 0.0670 chunk 231 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 243 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 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 206 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 40 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20104 Z= 0.206 Angle : 0.849 16.025 27268 Z= 0.386 Chirality : 0.045 0.168 3092 Planarity : 0.004 0.031 3448 Dihedral : 5.782 55.168 2700 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.50 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.90 (0.17), residues: 2436 helix: -0.34 (0.15), residues: 1184 sheet: -6.54 (0.09), residues: 56 loop : -1.95 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 613 HIS 0.003 0.001 HIS C 522 PHE 0.026 0.002 PHE B 504 TYR 0.023 0.001 TYR A 432 ARG 0.007 0.000 ARG B 589 ********************** 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 535 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 2.364 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: A 99 MET cc_start: 0.8893 (mmp) cc_final: 0.8489 (mmp) REVERT: A 110 MET cc_start: 0.8861 (mmm) cc_final: 0.7898 (mmm) REVERT: A 127 ASN cc_start: 0.8611 (m-40) cc_final: 0.8199 (p0) REVERT: A 209 LYS cc_start: 0.9632 (mtpt) cc_final: 0.9333 (mttt) REVERT: A 211 PHE cc_start: 0.8230 (t80) cc_final: 0.7764 (t80) REVERT: A 298 THR cc_start: 0.9031 (m) cc_final: 0.8780 (p) REVERT: A 315 GLU cc_start: 0.8597 (tp30) cc_final: 0.8351 (tp30) REVERT: A 318 SER cc_start: 0.9340 (t) cc_final: 0.8983 (p) REVERT: A 509 TYR cc_start: 0.8977 (t80) cc_final: 0.8475 (t80) REVERT: A 515 GLU cc_start: 0.8713 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 528 MET cc_start: 0.8695 (tpp) cc_final: 0.8157 (tpp) REVERT: A 556 SER cc_start: 0.9239 (m) cc_final: 0.8863 (p) REVERT: A 557 ILE cc_start: 0.9312 (pt) cc_final: 0.9004 (tt) REVERT: A 568 LEU cc_start: 0.9310 (tp) cc_final: 0.9004 (mm) REVERT: A 570 MET cc_start: 0.8095 (ppp) cc_final: 0.7808 (tmm) REVERT: B 92 LEU cc_start: 0.8671 (pt) cc_final: 0.8332 (tp) REVERT: B 110 MET cc_start: 0.8809 (mmm) cc_final: 0.7858 (tpp) REVERT: B 127 ASN cc_start: 0.8571 (m-40) cc_final: 0.8251 (p0) REVERT: B 209 LYS cc_start: 0.9619 (mtpt) cc_final: 0.9359 (mttt) REVERT: B 250 GLU cc_start: 0.8412 (tp30) cc_final: 0.8121 (tp30) REVERT: B 280 LEU cc_start: 0.9198 (tp) cc_final: 0.8858 (tp) REVERT: B 298 THR cc_start: 0.9021 (m) cc_final: 0.8773 (p) REVERT: B 497 MET cc_start: 0.8908 (tmm) cc_final: 0.8410 (tmm) REVERT: B 509 TYR cc_start: 0.8929 (t80) cc_final: 0.8430 (t80) REVERT: B 515 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 528 MET cc_start: 0.8546 (tpp) cc_final: 0.8215 (tpp) REVERT: B 556 SER cc_start: 0.9204 (m) cc_final: 0.8866 (p) REVERT: B 557 ILE cc_start: 0.9256 (pt) cc_final: 0.8983 (tt) REVERT: C 92 LEU cc_start: 0.8643 (pt) cc_final: 0.8330 (tp) REVERT: C 110 MET cc_start: 0.8844 (mmm) cc_final: 0.7819 (mmm) REVERT: C 127 ASN cc_start: 0.8571 (m-40) cc_final: 0.8229 (p0) REVERT: C 209 LYS cc_start: 0.9642 (mtpt) cc_final: 0.9366 (mttt) REVERT: C 211 PHE cc_start: 0.8242 (t80) cc_final: 0.7753 (t80) REVERT: C 250 GLU cc_start: 0.8450 (tp30) cc_final: 0.8123 (tp30) REVERT: C 280 LEU cc_start: 0.9191 (tp) cc_final: 0.8874 (tp) REVERT: C 298 THR cc_start: 0.9054 (m) cc_final: 0.8815 (p) REVERT: C 315 GLU cc_start: 0.8539 (tp30) cc_final: 0.8334 (tp30) REVERT: C 318 SER cc_start: 0.9360 (t) cc_final: 0.9011 (p) REVERT: C 367 LEU cc_start: 0.8815 (tt) cc_final: 0.7126 (tt) REVERT: C 454 MET cc_start: 0.8352 (tpp) cc_final: 0.7984 (tpp) REVERT: C 509 TYR cc_start: 0.9044 (t80) cc_final: 0.8452 (t80) REVERT: C 515 GLU cc_start: 0.8641 (mm-30) cc_final: 0.7995 (mm-30) REVERT: C 528 MET cc_start: 0.8576 (tpp) cc_final: 0.8085 (tpp) REVERT: C 556 SER cc_start: 0.9211 (m) cc_final: 0.8791 (p) REVERT: D 110 MET cc_start: 0.8785 (mmm) cc_final: 0.7851 (mmm) REVERT: D 209 LYS cc_start: 0.9633 (mtpt) cc_final: 0.9332 (mttt) REVERT: D 211 PHE cc_start: 0.8349 (t80) cc_final: 0.7691 (t80) REVERT: D 250 GLU cc_start: 0.8535 (tp30) cc_final: 0.8299 (mm-30) REVERT: D 280 LEU cc_start: 0.9184 (tp) cc_final: 0.8963 (tp) REVERT: D 315 GLU cc_start: 0.8566 (tp30) cc_final: 0.8353 (tp30) REVERT: D 318 SER cc_start: 0.9372 (t) cc_final: 0.9012 (p) REVERT: D 367 LEU cc_start: 0.8813 (tt) cc_final: 0.7112 (tt) REVERT: D 435 MET cc_start: 0.9171 (mmm) cc_final: 0.8847 (mmm) REVERT: D 485 MET cc_start: 0.8873 (mmt) cc_final: 0.8348 (mmt) REVERT: D 509 TYR cc_start: 0.8995 (t80) cc_final: 0.8421 (t80) REVERT: D 515 GLU cc_start: 0.8736 (mm-30) cc_final: 0.7821 (mm-30) REVERT: D 528 MET cc_start: 0.8563 (tpp) cc_final: 0.8231 (tpp) REVERT: D 556 SER cc_start: 0.9196 (m) cc_final: 0.8838 (p) REVERT: D 557 ILE cc_start: 0.9149 (pt) cc_final: 0.8859 (tt) REVERT: D 613 TRP cc_start: 0.8113 (t60) cc_final: 0.7872 (t60) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.2692 time to fit residues: 229.9976 Evaluate side-chains 448 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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: 0.7980 chunk 206 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 178 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 193 optimal weight: 0.4980 chunk 81 optimal weight: 0.0060 chunk 199 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- 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** A 587 HIS ** 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 37 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** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082703 restraints weight = 55113.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085178 restraints weight = 34220.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.086820 restraints weight = 24032.501| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20104 Z= 0.195 Angle : 0.840 14.657 27268 Z= 0.380 Chirality : 0.045 0.161 3092 Planarity : 0.004 0.031 3448 Dihedral : 5.674 57.457 2700 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.95 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2436 helix: -0.30 (0.15), residues: 1208 sheet: -6.58 (0.09), residues: 56 loop : -2.07 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 268 HIS 0.004 0.001 HIS C 587 PHE 0.019 0.001 PHE B 211 TYR 0.015 0.001 TYR C 432 ARG 0.007 0.000 ARG B 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4817.73 seconds wall clock time: 87 minutes 59.25 seconds (5279.25 seconds total)