Starting phenix.real_space_refine on Mon Mar 18 03:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/03_2024/7k4d_22665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/03_2024/7k4d_22665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/03_2024/7k4d_22665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/03_2024/7k4d_22665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/03_2024/7k4d_22665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/03_2024/7k4d_22665_neut_updated.pdb" } resolution = 3.66 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= 0.003 sd= 0.037 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 C 12811 2.51 5 N 3339 2.21 5 O 3474 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19801 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4911 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'VUM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'VUM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'VUM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'VUM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.60, per 1000 atoms: 0.48 Number of scatterers: 19801 At special positions: 0 Unit cell: (143.45, 143.45, 127.3, 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 F 15 9.00 O 3474 8.00 N 3339 7.00 C 12811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 3.6 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 51.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.528A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.729A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.576A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.826A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 removed outlier: 4.027A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.726A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.569A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.748A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 205' Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.765A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.608A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.700A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.093A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.676A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.895A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 removed outlier: 3.754A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.655A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 419 through 422 No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 424 through 444 removed outlier: 3.799A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.934A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.600A pdb=" N LYS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.724A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 removed outlier: 3.989A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 566 removed outlier: 3.930A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.634A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.982A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.528A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.730A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.576A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.826A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 4.028A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.726A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.568A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.748A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 205' Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.765A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 removed outlier: 3.607A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.700A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.093A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.677A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.896A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 348 removed outlier: 3.754A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 3.654A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 419 through 422 No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 424 through 444 removed outlier: 3.799A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 removed outlier: 3.933A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.600A pdb=" N LYS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.725A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.989A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 566 removed outlier: 3.930A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 584 removed outlier: 4.635A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.981A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.528A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 67 removed outlier: 3.729A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.575A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.826A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 removed outlier: 4.028A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.726A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.568A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.747A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 205' Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.765A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.608A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.699A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 4.093A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.676A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 309' Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.895A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 removed outlier: 3.754A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 406 removed outlier: 3.654A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 419 through 422 No H-bonds generated for 'chain 'C' and resid 419 through 422' Processing helix chain 'C' and resid 424 through 444 removed outlier: 3.799A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.935A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 469 Processing helix chain 'C' and resid 480 through 486 removed outlier: 3.600A pdb=" N LYS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.725A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 removed outlier: 3.990A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 566 removed outlier: 3.930A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 584 removed outlier: 4.634A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.981A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.528A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.729A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.577A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.825A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 4.027A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.726A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.568A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.747A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 199 through 205' Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.765A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 removed outlier: 3.608A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.700A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 removed outlier: 4.093A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.676A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 309' Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.895A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 347 removed outlier: 3.754A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 406 removed outlier: 3.654A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 419 through 422 No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 424 through 444 removed outlier: 3.799A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.934A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 469 Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.599A pdb=" N LYS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 511 removed outlier: 3.724A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 removed outlier: 3.989A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 removed outlier: 3.931A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 584 removed outlier: 4.634A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.982A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.521A pdb=" N THR A 274 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 633 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.521A pdb=" N THR B 274 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 633 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.520A pdb=" N THR C 274 " --> pdb=" O ASP C 635 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 633 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.521A pdb=" N THR D 274 " --> pdb=" O ASP D 635 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 633 " --> pdb=" O THR D 276 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1653 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: 4.62 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6275 1.34 - 1.46: 4339 1.46 - 1.58: 9380 1.58 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 20266 Sorted by residual: bond pdb=" C01 VUM D 702 " pdb=" O01 VUM D 702 " ideal model delta sigma weight residual 1.230 1.400 -0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" C01 VUM C 701 " pdb=" O01 VUM C 701 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C01 VUM B 701 " pdb=" O01 VUM B 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C01 VUM A 701 " pdb=" O01 VUM A 701 " ideal model delta sigma weight residual 1.230 1.391 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C01 VUM D 701 " pdb=" O01 VUM D 701 " ideal model delta sigma weight residual 1.230 1.391 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 20261 not shown) Histogram of bond angle deviations from ideal: 96.32 - 103.86: 351 103.86 - 111.41: 8027 111.41 - 118.95: 8155 118.95 - 126.49: 10637 126.49 - 134.04: 348 Bond angle restraints: 27518 Sorted by residual: angle pdb=" N VAL A 465 " pdb=" CA VAL A 465 " pdb=" C VAL A 465 " ideal model delta sigma weight residual 112.80 105.68 7.12 1.15e+00 7.56e-01 3.83e+01 angle pdb=" N VAL D 465 " pdb=" CA VAL D 465 " pdb=" C VAL D 465 " ideal model delta sigma weight residual 112.80 105.70 7.10 1.15e+00 7.56e-01 3.81e+01 angle pdb=" N VAL B 465 " pdb=" CA VAL B 465 " pdb=" C VAL B 465 " ideal model delta sigma weight residual 112.80 105.71 7.09 1.15e+00 7.56e-01 3.80e+01 angle pdb=" N VAL C 465 " pdb=" CA VAL C 465 " pdb=" C VAL C 465 " ideal model delta sigma weight residual 112.80 105.73 7.07 1.15e+00 7.56e-01 3.78e+01 angle pdb=" N LEU C 372 " pdb=" CA LEU C 372 " pdb=" C LEU C 372 " ideal model delta sigma weight residual 110.24 117.43 -7.19 1.30e+00 5.92e-01 3.06e+01 ... (remaining 27513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.26: 11652 23.26 - 46.52: 530 46.52 - 69.78: 25 69.78 - 93.03: 9 93.03 - 116.29: 7 Dihedral angle restraints: 12223 sinusoidal: 5063 harmonic: 7160 Sorted by residual: dihedral pdb=" CA ILE D 540 " pdb=" C ILE D 540 " pdb=" N ILE D 541 " pdb=" CA ILE D 541 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE A 540 " pdb=" C ILE A 540 " pdb=" N ILE A 541 " pdb=" CA ILE A 541 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE C 540 " pdb=" C ILE C 540 " pdb=" N ILE C 541 " pdb=" CA ILE C 541 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 12220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1962 0.048 - 0.097: 898 0.097 - 0.145: 195 0.145 - 0.193: 27 0.193 - 0.241: 28 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CB ILE B 540 " pdb=" CA ILE B 540 " pdb=" CG1 ILE B 540 " pdb=" CG2 ILE B 540 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE D 540 " pdb=" CA ILE D 540 " pdb=" CG1 ILE D 540 " pdb=" CG2 ILE D 540 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 3107 not shown) Planarity restraints: 3458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 476 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO D 477 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 477 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 477 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO C 477 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 477 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " 0.048 5.00e-02 4.00e+02 ... (remaining 3455 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2575 2.74 - 3.28: 18466 3.28 - 3.82: 30030 3.82 - 4.36: 34996 4.36 - 4.90: 57990 Nonbonded interactions: 144057 Sorted by model distance: nonbonded pdb=" OH TYR C 623 " pdb=" OE2 GLU D 35 " model vdw 2.205 2.440 nonbonded pdb=" NE2 GLN A 118 " pdb=" OH TYR D 270 " model vdw 2.337 2.520 nonbonded pdb=" OH TYR A 623 " pdb=" OE2 GLU B 35 " model vdw 2.357 2.440 nonbonded pdb=" OH TYR B 623 " pdb=" OE2 GLU C 35 " model vdw 2.379 2.440 nonbonded pdb=" O TYR A 349 " pdb=" NH1 ARG A 385 " model vdw 2.400 2.520 ... (remaining 144052 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 639 or resid 701)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 28 through 639 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 4.680 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 47.010 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 0.170 20266 Z= 0.622 Angle : 1.216 11.157 27518 Z= 0.661 Chirality : 0.058 0.241 3110 Planarity : 0.008 0.087 3458 Dihedral : 12.492 116.292 7599 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.38 % Allowed : 6.59 % Favored : 93.03 % 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: -6.15 (0.11), residues: 2440 helix: -4.58 (0.06), residues: 1224 sheet: -2.92 (0.59), residues: 56 loop : -3.52 (0.15), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 321 HIS 0.020 0.002 HIS A 522 PHE 0.028 0.003 PHE A 162 TYR 0.021 0.002 TYR A 547 ARG 0.008 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 636 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7848 (m110) cc_final: 0.6836 (t0) REVERT: A 84 HIS cc_start: 0.7949 (m90) cc_final: 0.7552 (m90) REVERT: A 91 ASN cc_start: 0.8037 (m110) cc_final: 0.7689 (m-40) REVERT: A 96 MET cc_start: 0.7936 (tmm) cc_final: 0.7315 (tmm) REVERT: A 100 GLU cc_start: 0.8419 (tp30) cc_final: 0.8153 (mt-10) REVERT: A 128 GLN cc_start: 0.7106 (pt0) cc_final: 0.6403 (tm-30) REVERT: A 146 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7542 (tpp-160) REVERT: A 214 GLN cc_start: 0.8188 (mt0) cc_final: 0.7298 (tm-30) REVERT: A 250 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8138 (tp30) REVERT: A 262 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8519 (tptt) REVERT: A 284 ASP cc_start: 0.8914 (t70) cc_final: 0.8654 (t0) REVERT: A 300 LYS cc_start: 0.8437 (pmtt) cc_final: 0.7896 (ttmt) REVERT: A 303 GLU cc_start: 0.8369 (tt0) cc_final: 0.8094 (tt0) REVERT: A 440 MET cc_start: 0.8906 (ttp) cc_final: 0.7912 (mmp) REVERT: A 470 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.8259 (ptp90) REVERT: A 502 LEU cc_start: 0.8291 (tp) cc_final: 0.7922 (tt) REVERT: A 547 TYR cc_start: 0.8068 (m-10) cc_final: 0.7755 (m-10) REVERT: A 577 MET cc_start: 0.7297 (mtp) cc_final: 0.6963 (mtp) REVERT: A 619 CYS cc_start: 0.7777 (p) cc_final: 0.7396 (p) REVERT: A 637 GLN cc_start: 0.8547 (tp40) cc_final: 0.8277 (tt0) REVERT: B 34 ASP cc_start: 0.8167 (m-30) cc_final: 0.7942 (m-30) REVERT: B 62 ASN cc_start: 0.7843 (m110) cc_final: 0.6698 (t0) REVERT: B 84 HIS cc_start: 0.8017 (m90) cc_final: 0.7569 (m90) REVERT: B 91 ASN cc_start: 0.8064 (m110) cc_final: 0.7649 (m-40) REVERT: B 96 MET cc_start: 0.8004 (tmm) cc_final: 0.7290 (tmm) REVERT: B 100 GLU cc_start: 0.8425 (tp30) cc_final: 0.8175 (mt-10) REVERT: B 128 GLN cc_start: 0.7067 (pt0) cc_final: 0.6181 (pp30) REVERT: B 144 SER cc_start: 0.8115 (m) cc_final: 0.7600 (p) REVERT: B 146 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7546 (tpp-160) REVERT: B 214 GLN cc_start: 0.8289 (mt0) cc_final: 0.7448 (tm-30) REVERT: B 250 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8123 (tp30) REVERT: B 270 TYR cc_start: 0.7923 (t80) cc_final: 0.7485 (t80) REVERT: B 300 LYS cc_start: 0.8308 (pmtt) cc_final: 0.7808 (ttmt) REVERT: B 303 GLU cc_start: 0.8391 (tt0) cc_final: 0.8154 (tt0) REVERT: B 368 LEU cc_start: 0.6348 (mp) cc_final: 0.6058 (mp) REVERT: B 440 MET cc_start: 0.8910 (ttp) cc_final: 0.8028 (mmp) REVERT: B 464 ASN cc_start: 0.7377 (t0) cc_final: 0.6795 (t0) REVERT: B 470 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.8237 (ptp90) REVERT: B 502 LEU cc_start: 0.8329 (tp) cc_final: 0.7961 (tt) REVERT: B 577 MET cc_start: 0.7317 (mtp) cc_final: 0.7045 (ttm) REVERT: B 637 GLN cc_start: 0.8559 (tp40) cc_final: 0.8337 (tt0) REVERT: C 59 GLN cc_start: 0.8358 (tp-100) cc_final: 0.8031 (tp-100) REVERT: C 62 ASN cc_start: 0.7929 (m110) cc_final: 0.6898 (t0) REVERT: C 71 LYS cc_start: 0.7226 (mttt) cc_final: 0.6437 (mmpt) REVERT: C 84 HIS cc_start: 0.8217 (m90) cc_final: 0.7648 (m90) REVERT: C 91 ASN cc_start: 0.7860 (m110) cc_final: 0.7453 (m-40) REVERT: C 144 SER cc_start: 0.8288 (m) cc_final: 0.7772 (p) REVERT: C 146 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7347 (tpp-160) REVERT: C 193 ASP cc_start: 0.7305 (p0) cc_final: 0.6625 (p0) REVERT: C 214 GLN cc_start: 0.8237 (mt0) cc_final: 0.7683 (tm-30) REVERT: C 250 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7684 (tp30) REVERT: C 262 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8571 (tptt) REVERT: C 294 GLU cc_start: 0.8018 (tp30) cc_final: 0.7582 (tt0) REVERT: C 315 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7944 (tp30) REVERT: C 355 ARG cc_start: 0.7754 (ttt-90) cc_final: 0.7239 (ttt-90) REVERT: C 440 MET cc_start: 0.8875 (ttp) cc_final: 0.7737 (tpt) REVERT: C 481 MET cc_start: 0.7802 (tpp) cc_final: 0.7426 (tpp) REVERT: C 546 ASN cc_start: 0.8596 (t0) cc_final: 0.8161 (t0) REVERT: C 578 MET cc_start: 0.8271 (mmt) cc_final: 0.7528 (mmt) REVERT: C 637 GLN cc_start: 0.8596 (tp40) cc_final: 0.8340 (tt0) REVERT: D 34 ASP cc_start: 0.8173 (m-30) cc_final: 0.7960 (m-30) REVERT: D 62 ASN cc_start: 0.7767 (m110) cc_final: 0.6733 (t0) REVERT: D 84 HIS cc_start: 0.8247 (m90) cc_final: 0.7825 (m90) REVERT: D 91 ASN cc_start: 0.8242 (m110) cc_final: 0.7839 (m-40) REVERT: D 96 MET cc_start: 0.8098 (tmm) cc_final: 0.7825 (tmm) REVERT: D 100 GLU cc_start: 0.8381 (tp30) cc_final: 0.8070 (mt-10) REVERT: D 128 GLN cc_start: 0.7006 (pt0) cc_final: 0.6606 (pp30) REVERT: D 137 LEU cc_start: 0.9244 (mt) cc_final: 0.8919 (tt) REVERT: D 144 SER cc_start: 0.8173 (m) cc_final: 0.7669 (p) REVERT: D 146 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7622 (tpp-160) REVERT: D 193 ASP cc_start: 0.7610 (p0) cc_final: 0.7198 (p0) REVERT: D 214 GLN cc_start: 0.8318 (mt0) cc_final: 0.7368 (tm-30) REVERT: D 250 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8161 (tp30) REVERT: D 262 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8593 (mmtt) REVERT: D 268 TRP cc_start: 0.8182 (p-90) cc_final: 0.7803 (p-90) REVERT: D 282 GLU cc_start: 0.7408 (tt0) cc_final: 0.6921 (tt0) REVERT: D 303 GLU cc_start: 0.8370 (tt0) cc_final: 0.8099 (tt0) REVERT: D 323 ARG cc_start: 0.8279 (ptt180) cc_final: 0.7818 (ptt90) REVERT: D 440 MET cc_start: 0.8891 (ttp) cc_final: 0.7824 (mmp) REVERT: D 502 LEU cc_start: 0.8499 (tp) cc_final: 0.8216 (tt) REVERT: D 637 GLN cc_start: 0.8442 (tp40) cc_final: 0.8242 (tt0) outliers start: 8 outliers final: 0 residues processed: 636 average time/residue: 0.3284 time to fit residues: 310.1941 Evaluate side-chains 445 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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: 4.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 165 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 357 ASN A 358 ASN A 464 ASN A 548 ASN A 596 GLN B 59 GLN B 118 GLN B 165 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 357 ASN B 358 ASN B 464 ASN B 548 ASN B 596 GLN C 118 GLN C 128 GLN C 165 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 357 ASN C 358 ASN C 464 ASN C 473 GLN C 548 ASN C 582 HIS C 596 GLN D 118 GLN D 165 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 357 ASN D 358 ASN D 464 ASN D 473 GLN D 548 ASN D 596 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20266 Z= 0.172 Angle : 0.662 8.960 27518 Z= 0.340 Chirality : 0.040 0.170 3110 Planarity : 0.005 0.066 3458 Dihedral : 7.771 86.905 2879 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.30 % Allowed : 12.52 % Favored : 84.18 % 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: -4.83 (0.13), residues: 2440 helix: -2.99 (0.11), residues: 1340 sheet: -2.58 (0.62), residues: 56 loop : -3.44 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 321 HIS 0.007 0.001 HIS B 522 PHE 0.013 0.001 PHE C 504 TYR 0.018 0.001 TYR D 623 ARG 0.007 0.000 ARG C 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 493 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7726 (m110) cc_final: 0.6696 (t0) REVERT: A 71 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7213 (mmpt) REVERT: A 91 ASN cc_start: 0.7954 (m110) cc_final: 0.7500 (m-40) REVERT: A 128 GLN cc_start: 0.7142 (pt0) cc_final: 0.6398 (tm-30) REVERT: A 214 GLN cc_start: 0.8088 (mt0) cc_final: 0.7242 (tm-30) REVERT: A 250 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8227 (tp30) REVERT: A 262 LYS cc_start: 0.8839 (tmtt) cc_final: 0.8587 (tptt) REVERT: A 282 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 284 ASP cc_start: 0.8778 (t70) cc_final: 0.8472 (t0) REVERT: A 300 LYS cc_start: 0.8276 (pmtt) cc_final: 0.7871 (ttmt) REVERT: A 303 GLU cc_start: 0.8390 (tt0) cc_final: 0.8158 (tt0) REVERT: A 315 GLU cc_start: 0.7991 (tp30) cc_final: 0.7588 (mm-30) REVERT: A 378 MET cc_start: 0.7519 (ttm) cc_final: 0.6980 (ttt) REVERT: A 440 MET cc_start: 0.8380 (ttp) cc_final: 0.7632 (tpt) REVERT: A 470 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.8332 (ptp-170) REVERT: A 502 LEU cc_start: 0.8112 (tp) cc_final: 0.7852 (tt) REVERT: A 570 MET cc_start: 0.8498 (tpp) cc_final: 0.8240 (tpt) REVERT: A 574 LEU cc_start: 0.5115 (OUTLIER) cc_final: 0.4585 (mm) REVERT: A 621 ARG cc_start: 0.6544 (ptt-90) cc_final: 0.6261 (ttp80) REVERT: A 629 TRP cc_start: 0.5677 (m-10) cc_final: 0.4999 (m-10) REVERT: A 637 GLN cc_start: 0.8433 (tp40) cc_final: 0.8142 (tt0) REVERT: B 38 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8179 (tt) REVERT: B 62 ASN cc_start: 0.7674 (m110) cc_final: 0.6679 (t0) REVERT: B 71 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7143 (mmpt) REVERT: B 91 ASN cc_start: 0.7947 (m110) cc_final: 0.7507 (m-40) REVERT: B 128 GLN cc_start: 0.6968 (pt0) cc_final: 0.6320 (tm-30) REVERT: B 164 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 214 GLN cc_start: 0.8249 (mt0) cc_final: 0.7344 (tm-30) REVERT: B 250 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8244 (tp30) REVERT: B 300 LYS cc_start: 0.8187 (pmtt) cc_final: 0.7804 (ttmt) REVERT: B 303 GLU cc_start: 0.8380 (tt0) cc_final: 0.8171 (tt0) REVERT: B 315 GLU cc_start: 0.7950 (tp30) cc_final: 0.7514 (mm-30) REVERT: B 440 MET cc_start: 0.8559 (ttp) cc_final: 0.7847 (tpt) REVERT: B 464 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.6730 (t0) REVERT: B 470 ARG cc_start: 0.8511 (ptp-170) cc_final: 0.8246 (ptp-170) REVERT: B 481 MET cc_start: 0.7724 (tpp) cc_final: 0.7170 (tpp) REVERT: B 570 MET cc_start: 0.8623 (tpp) cc_final: 0.8315 (tpt) REVERT: B 577 MET cc_start: 0.6897 (mtp) cc_final: 0.6684 (ttm) REVERT: B 637 GLN cc_start: 0.8419 (tp40) cc_final: 0.8138 (tt0) REVERT: C 38 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8116 (tt) REVERT: C 59 GLN cc_start: 0.8276 (tp-100) cc_final: 0.8050 (tp-100) REVERT: C 62 ASN cc_start: 0.7688 (m110) cc_final: 0.6777 (t0) REVERT: C 71 LYS cc_start: 0.7188 (mttt) cc_final: 0.6836 (mmtt) REVERT: C 84 HIS cc_start: 0.7800 (m90) cc_final: 0.7350 (m90) REVERT: C 180 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8374 (ttm170) REVERT: C 214 GLN cc_start: 0.8201 (mt0) cc_final: 0.7478 (tm-30) REVERT: C 215 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8607 (ttt) REVERT: C 216 TYR cc_start: 0.9133 (t80) cc_final: 0.8889 (t80) REVERT: C 250 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8031 (tp30) REVERT: C 262 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8372 (tptt) REVERT: C 268 TRP cc_start: 0.8224 (p-90) cc_final: 0.7946 (p-90) REVERT: C 294 GLU cc_start: 0.7669 (tp30) cc_final: 0.7272 (tt0) REVERT: C 440 MET cc_start: 0.8534 (ttp) cc_final: 0.7462 (tpt) REVERT: C 454 MET cc_start: 0.7959 (tpp) cc_final: 0.7436 (tpt) REVERT: C 464 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7415 (t0) REVERT: C 470 ARG cc_start: 0.8367 (ptp-170) cc_final: 0.8115 (ptp-170) REVERT: C 536 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7600 (tt) REVERT: C 542 ASP cc_start: 0.7828 (m-30) cc_final: 0.7439 (m-30) REVERT: C 546 ASN cc_start: 0.8449 (t0) cc_final: 0.8246 (t0) REVERT: C 574 LEU cc_start: 0.4670 (OUTLIER) cc_final: 0.3504 (tt) REVERT: C 578 MET cc_start: 0.8023 (mmt) cc_final: 0.7316 (mmt) REVERT: C 584 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7764 (ttp-110) REVERT: C 622 GLU cc_start: 0.8534 (tp30) cc_final: 0.8332 (mt-10) REVERT: C 637 GLN cc_start: 0.8521 (tp40) cc_final: 0.8236 (tt0) REVERT: D 71 LYS cc_start: 0.7404 (mtpt) cc_final: 0.7072 (mtpt) REVERT: D 84 HIS cc_start: 0.7870 (m90) cc_final: 0.7565 (m90) REVERT: D 91 ASN cc_start: 0.8043 (m110) cc_final: 0.7744 (m-40) REVERT: D 164 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: D 193 ASP cc_start: 0.7977 (p0) cc_final: 0.7254 (p0) REVERT: D 214 GLN cc_start: 0.8256 (mt0) cc_final: 0.7422 (tm-30) REVERT: D 250 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8244 (tp30) REVERT: D 262 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8573 (tptt) REVERT: D 300 LYS cc_start: 0.8301 (pmtt) cc_final: 0.7877 (ttmt) REVERT: D 303 GLU cc_start: 0.8385 (tt0) cc_final: 0.8146 (tt0) REVERT: D 331 MET cc_start: 0.5007 (ttp) cc_final: 0.4397 (tmm) REVERT: D 440 MET cc_start: 0.8400 (ttp) cc_final: 0.7558 (tpt) REVERT: D 454 MET cc_start: 0.8326 (tpp) cc_final: 0.7709 (tpt) REVERT: D 464 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.6593 (t0) REVERT: D 570 MET cc_start: 0.8281 (tpp) cc_final: 0.7943 (tpt) REVERT: D 578 MET cc_start: 0.8545 (mmt) cc_final: 0.8189 (mmt) REVERT: D 629 TRP cc_start: 0.5239 (m-10) cc_final: 0.4757 (m-10) REVERT: D 637 GLN cc_start: 0.8420 (tp40) cc_final: 0.8104 (tt0) outliers start: 70 outliers final: 20 residues processed: 541 average time/residue: 0.3028 time to fit residues: 249.4587 Evaluate side-chains 446 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 414 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 464 ASN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN B 59 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN B 572 ASN C 129 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20266 Z= 0.221 Angle : 0.652 9.262 27518 Z= 0.327 Chirality : 0.041 0.170 3110 Planarity : 0.004 0.054 3458 Dihedral : 7.076 61.879 2879 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.48 % Allowed : 15.73 % Favored : 80.79 % 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: -3.71 (0.15), residues: 2440 helix: -2.00 (0.13), residues: 1312 sheet: -2.46 (0.62), residues: 56 loop : -3.03 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 268 HIS 0.006 0.001 HIS B 522 PHE 0.017 0.001 PHE A 553 TYR 0.028 0.001 TYR D 324 ARG 0.006 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 445 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7744 (m110) cc_final: 0.6790 (t0) REVERT: A 71 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7050 (mmpt) REVERT: A 91 ASN cc_start: 0.7886 (m110) cc_final: 0.7542 (m-40) REVERT: A 99 MET cc_start: 0.7940 (mmm) cc_final: 0.7466 (mmm) REVERT: A 100 GLU cc_start: 0.8361 (tp30) cc_final: 0.7896 (mt-10) REVERT: A 180 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8034 (ttm-80) REVERT: A 214 GLN cc_start: 0.8206 (mt0) cc_final: 0.7326 (tm-30) REVERT: A 239 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6087 (tm-30) REVERT: A 250 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8220 (tp30) REVERT: A 262 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8567 (tptt) REVERT: A 282 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 284 ASP cc_start: 0.8841 (t70) cc_final: 0.8555 (t0) REVERT: A 294 GLU cc_start: 0.7744 (tp30) cc_final: 0.7407 (mt-10) REVERT: A 300 LYS cc_start: 0.8257 (pmtt) cc_final: 0.7872 (ttmt) REVERT: A 303 GLU cc_start: 0.8424 (tt0) cc_final: 0.8193 (tt0) REVERT: A 378 MET cc_start: 0.7701 (ttm) cc_final: 0.7119 (ttt) REVERT: A 440 MET cc_start: 0.8489 (ttp) cc_final: 0.7606 (tpt) REVERT: A 637 GLN cc_start: 0.8398 (tp40) cc_final: 0.8101 (tt0) REVERT: B 62 ASN cc_start: 0.7697 (m110) cc_final: 0.6778 (t0) REVERT: B 71 LYS cc_start: 0.7522 (mtpt) cc_final: 0.7026 (mmpt) REVERT: B 91 ASN cc_start: 0.7901 (m110) cc_final: 0.7544 (m-40) REVERT: B 99 MET cc_start: 0.8042 (mmm) cc_final: 0.7728 (mmm) REVERT: B 164 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: B 180 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8266 (ttm-80) REVERT: B 214 GLN cc_start: 0.8285 (mt0) cc_final: 0.7355 (tm-30) REVERT: B 239 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: B 250 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8276 (tp30) REVERT: B 300 LYS cc_start: 0.8244 (pmtt) cc_final: 0.7816 (ttmt) REVERT: B 303 GLU cc_start: 0.8420 (tt0) cc_final: 0.8148 (tt0) REVERT: B 315 GLU cc_start: 0.8013 (tp30) cc_final: 0.7553 (mm-30) REVERT: B 440 MET cc_start: 0.8526 (ttp) cc_final: 0.7714 (tpt) REVERT: B 464 ASN cc_start: 0.7501 (t0) cc_final: 0.6811 (t0) REVERT: B 470 ARG cc_start: 0.8624 (ptp-170) cc_final: 0.8398 (ptp-170) REVERT: B 574 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.4200 (mt) REVERT: B 637 GLN cc_start: 0.8299 (tp40) cc_final: 0.8057 (tt0) REVERT: C 38 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8146 (tt) REVERT: C 62 ASN cc_start: 0.7827 (m110) cc_final: 0.6959 (t0) REVERT: C 71 LYS cc_start: 0.7408 (mttt) cc_final: 0.6749 (mmpt) REVERT: C 84 HIS cc_start: 0.7837 (m90) cc_final: 0.7378 (m90) REVERT: C 99 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7118 (tmm) REVERT: C 180 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8271 (ttm170) REVERT: C 214 GLN cc_start: 0.8239 (mt0) cc_final: 0.7398 (tm-30) REVERT: C 215 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8644 (ttt) REVERT: C 239 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: C 250 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8075 (tp30) REVERT: C 262 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8376 (tptt) REVERT: C 268 TRP cc_start: 0.8225 (p-90) cc_final: 0.7944 (p-90) REVERT: C 294 GLU cc_start: 0.7779 (tp30) cc_final: 0.7286 (tt0) REVERT: C 440 MET cc_start: 0.8529 (ttp) cc_final: 0.7521 (tpt) REVERT: C 464 ASN cc_start: 0.7809 (t0) cc_final: 0.7165 (t0) REVERT: C 470 ARG cc_start: 0.8410 (ptp-170) cc_final: 0.8165 (ptp-170) REVERT: C 536 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7622 (tt) REVERT: C 542 ASP cc_start: 0.7814 (m-30) cc_final: 0.7270 (m-30) REVERT: C 574 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4149 (tp) REVERT: C 637 GLN cc_start: 0.8509 (tp40) cc_final: 0.8218 (tt0) REVERT: D 71 LYS cc_start: 0.7434 (mtpt) cc_final: 0.7133 (mtpt) REVERT: D 84 HIS cc_start: 0.7987 (m90) cc_final: 0.7538 (m90) REVERT: D 91 ASN cc_start: 0.7926 (m110) cc_final: 0.7591 (m-40) REVERT: D 99 MET cc_start: 0.8092 (mmm) cc_final: 0.7835 (mmm) REVERT: D 164 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: D 193 ASP cc_start: 0.8042 (p0) cc_final: 0.7364 (p0) REVERT: D 214 GLN cc_start: 0.8244 (mt0) cc_final: 0.7368 (tm-30) REVERT: D 239 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6130 (tm-30) REVERT: D 250 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8260 (tp30) REVERT: D 262 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8620 (tptt) REVERT: D 294 GLU cc_start: 0.7734 (tp30) cc_final: 0.7448 (mt-10) REVERT: D 300 LYS cc_start: 0.8353 (pmtt) cc_final: 0.7892 (ttmt) REVERT: D 303 GLU cc_start: 0.8377 (tt0) cc_final: 0.8123 (tt0) REVERT: D 440 MET cc_start: 0.8533 (ttp) cc_final: 0.7474 (tpt) REVERT: D 464 ASN cc_start: 0.7656 (t0) cc_final: 0.6737 (t0) REVERT: D 574 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.4030 (mt) REVERT: D 577 MET cc_start: 0.7788 (mtm) cc_final: 0.7472 (ttm) REVERT: D 578 MET cc_start: 0.8453 (mmt) cc_final: 0.8075 (mmt) REVERT: D 629 TRP cc_start: 0.5379 (m-10) cc_final: 0.4827 (m-10) REVERT: D 637 GLN cc_start: 0.8427 (tp40) cc_final: 0.8137 (tt0) outliers start: 74 outliers final: 29 residues processed: 485 average time/residue: 0.2924 time to fit residues: 218.6955 Evaluate side-chains 451 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 409 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20266 Z= 0.169 Angle : 0.603 9.892 27518 Z= 0.299 Chirality : 0.039 0.152 3110 Planarity : 0.004 0.053 3458 Dihedral : 6.361 42.679 2879 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.77 % Allowed : 17.14 % Favored : 79.10 % 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: -2.94 (0.16), residues: 2440 helix: -1.23 (0.14), residues: 1264 sheet: -2.13 (0.66), residues: 56 loop : -2.82 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.004 0.001 HIS B 522 PHE 0.011 0.001 PHE D 504 TYR 0.023 0.001 TYR A 324 ARG 0.007 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 454 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7788 (m110) cc_final: 0.6859 (t0) REVERT: A 71 LYS cc_start: 0.7518 (mtpt) cc_final: 0.7050 (mmpt) REVERT: A 91 ASN cc_start: 0.7865 (m110) cc_final: 0.7539 (m-40) REVERT: A 99 MET cc_start: 0.7935 (mmm) cc_final: 0.7523 (mmm) REVERT: A 144 SER cc_start: 0.8246 (m) cc_final: 0.7719 (p) REVERT: A 180 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8203 (ttm-80) REVERT: A 239 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6005 (tm-30) REVERT: A 250 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8296 (tp30) REVERT: A 262 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8397 (tptt) REVERT: A 282 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 284 ASP cc_start: 0.8852 (t70) cc_final: 0.8580 (t0) REVERT: A 294 GLU cc_start: 0.7793 (tp30) cc_final: 0.7517 (tt0) REVERT: A 300 LYS cc_start: 0.8259 (pmtt) cc_final: 0.7868 (ttmt) REVERT: A 303 GLU cc_start: 0.8412 (tt0) cc_final: 0.8142 (tt0) REVERT: A 355 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6337 (ptm-80) REVERT: A 378 MET cc_start: 0.7765 (ttm) cc_final: 0.7157 (ttt) REVERT: A 440 MET cc_start: 0.8486 (ttp) cc_final: 0.7805 (tpp) REVERT: A 454 MET cc_start: 0.8189 (tpp) cc_final: 0.7944 (tpt) REVERT: A 574 LEU cc_start: 0.5133 (OUTLIER) cc_final: 0.3574 (mt) REVERT: A 637 GLN cc_start: 0.8278 (tp40) cc_final: 0.7963 (tt0) REVERT: B 62 ASN cc_start: 0.7695 (m110) cc_final: 0.6804 (t0) REVERT: B 71 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7077 (mmpt) REVERT: B 91 ASN cc_start: 0.7854 (m110) cc_final: 0.7514 (m-40) REVERT: B 99 MET cc_start: 0.8015 (mmm) cc_final: 0.7707 (mmm) REVERT: B 164 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: B 214 GLN cc_start: 0.8225 (mt0) cc_final: 0.7410 (tm-30) REVERT: B 239 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6158 (tm-30) REVERT: B 250 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8289 (tp30) REVERT: B 270 TYR cc_start: 0.8011 (t80) cc_final: 0.7770 (t80) REVERT: B 282 GLU cc_start: 0.8238 (tp30) cc_final: 0.7897 (tp30) REVERT: B 300 LYS cc_start: 0.8298 (pmtt) cc_final: 0.7856 (ttmt) REVERT: B 303 GLU cc_start: 0.8422 (tt0) cc_final: 0.8177 (tt0) REVERT: B 315 GLU cc_start: 0.8001 (tp30) cc_final: 0.7517 (mm-30) REVERT: B 324 TYR cc_start: 0.7280 (m-80) cc_final: 0.7018 (m-80) REVERT: B 440 MET cc_start: 0.8544 (ttp) cc_final: 0.7862 (tpp) REVERT: B 454 MET cc_start: 0.8535 (tpp) cc_final: 0.8286 (tpt) REVERT: B 464 ASN cc_start: 0.7567 (t0) cc_final: 0.7145 (t0) REVERT: B 540 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7586 (tt) REVERT: B 542 ASP cc_start: 0.7893 (m-30) cc_final: 0.7402 (m-30) REVERT: B 574 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4364 (mp) REVERT: B 637 GLN cc_start: 0.8315 (tp40) cc_final: 0.8023 (tt0) REVERT: C 62 ASN cc_start: 0.7817 (m110) cc_final: 0.7025 (t0) REVERT: C 71 LYS cc_start: 0.7374 (mttt) cc_final: 0.6761 (mmpt) REVERT: C 99 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7090 (tmm) REVERT: C 180 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8113 (ttm110) REVERT: C 214 GLN cc_start: 0.8211 (mt0) cc_final: 0.7394 (tm-30) REVERT: C 215 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8663 (ttt) REVERT: C 239 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: C 250 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8082 (tp30) REVERT: C 262 LYS cc_start: 0.8707 (tmtt) cc_final: 0.8386 (tptt) REVERT: C 268 TRP cc_start: 0.8191 (p-90) cc_final: 0.7939 (p-90) REVERT: C 294 GLU cc_start: 0.7838 (tp30) cc_final: 0.7418 (tt0) REVERT: C 414 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7465 (tpp80) REVERT: C 440 MET cc_start: 0.8499 (ttp) cc_final: 0.7478 (tpt) REVERT: C 464 ASN cc_start: 0.7877 (t0) cc_final: 0.7507 (t0) REVERT: C 470 ARG cc_start: 0.8401 (ptp-170) cc_final: 0.8092 (ptp-170) REVERT: C 481 MET cc_start: 0.7137 (tpp) cc_final: 0.6913 (tpt) REVERT: C 536 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7580 (tt) REVERT: C 542 ASP cc_start: 0.7806 (m-30) cc_final: 0.7234 (m-30) REVERT: C 634 GLU cc_start: 0.8424 (pm20) cc_final: 0.7621 (mp0) REVERT: C 637 GLN cc_start: 0.8322 (tp40) cc_final: 0.8009 (tt0) REVERT: D 84 HIS cc_start: 0.7918 (m90) cc_final: 0.7476 (m90) REVERT: D 91 ASN cc_start: 0.7866 (m110) cc_final: 0.7525 (m-40) REVERT: D 164 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: D 193 ASP cc_start: 0.8038 (p0) cc_final: 0.7358 (p0) REVERT: D 214 GLN cc_start: 0.8247 (mt0) cc_final: 0.7259 (tm-30) REVERT: D 239 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: D 250 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8305 (tp30) REVERT: D 262 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8525 (tptt) REVERT: D 303 GLU cc_start: 0.8373 (tt0) cc_final: 0.8151 (tt0) REVERT: D 440 MET cc_start: 0.8419 (ttp) cc_final: 0.7664 (tpp) REVERT: D 464 ASN cc_start: 0.7536 (t0) cc_final: 0.6881 (t0) REVERT: D 559 TYR cc_start: 0.8201 (t80) cc_final: 0.7835 (t80) REVERT: D 574 LEU cc_start: 0.5355 (OUTLIER) cc_final: 0.4691 (mp) REVERT: D 577 MET cc_start: 0.7694 (mtm) cc_final: 0.7386 (ttm) REVERT: D 578 MET cc_start: 0.8421 (mmt) cc_final: 0.7921 (mmt) REVERT: D 629 TRP cc_start: 0.5326 (m-10) cc_final: 0.4904 (m-10) REVERT: D 637 GLN cc_start: 0.8347 (tp40) cc_final: 0.8040 (tt0) outliers start: 80 outliers final: 31 residues processed: 501 average time/residue: 0.2978 time to fit residues: 231.7229 Evaluate side-chains 465 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 420 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20266 Z= 0.280 Angle : 0.673 9.453 27518 Z= 0.329 Chirality : 0.043 0.269 3110 Planarity : 0.004 0.048 3458 Dihedral : 6.484 48.286 2879 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.57 % Allowed : 18.97 % Favored : 76.46 % 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: -2.66 (0.16), residues: 2440 helix: -0.95 (0.14), residues: 1256 sheet: -2.14 (0.66), residues: 56 loop : -2.72 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 629 HIS 0.006 0.001 HIS B 522 PHE 0.012 0.002 PHE A 211 TYR 0.026 0.002 TYR D 324 ARG 0.008 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 442 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7804 (m110) cc_final: 0.6906 (t0) REVERT: A 71 LYS cc_start: 0.7482 (mtpt) cc_final: 0.7025 (mmpt) REVERT: A 84 HIS cc_start: 0.7694 (m90) cc_final: 0.7343 (m90) REVERT: A 91 ASN cc_start: 0.7942 (m110) cc_final: 0.7628 (m-40) REVERT: A 99 MET cc_start: 0.7996 (mmm) cc_final: 0.7585 (mmm) REVERT: A 144 SER cc_start: 0.8357 (m) cc_final: 0.7750 (p) REVERT: A 214 GLN cc_start: 0.8182 (mt0) cc_final: 0.7337 (tm-30) REVERT: A 239 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: A 250 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8194 (tp30) REVERT: A 262 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8506 (tptt) REVERT: A 282 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7818 (mt-10) REVERT: A 294 GLU cc_start: 0.7864 (tp30) cc_final: 0.7437 (tt0) REVERT: A 300 LYS cc_start: 0.8344 (pmtt) cc_final: 0.7883 (ttmt) REVERT: A 303 GLU cc_start: 0.8455 (tt0) cc_final: 0.7971 (tt0) REVERT: A 378 MET cc_start: 0.7937 (ttm) cc_final: 0.7379 (ttt) REVERT: A 440 MET cc_start: 0.8473 (ttp) cc_final: 0.7524 (tpt) REVERT: A 454 MET cc_start: 0.8142 (tpp) cc_final: 0.7838 (tpt) REVERT: A 490 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6569 (tt) REVERT: A 540 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 564 ILE cc_start: 0.7778 (tp) cc_final: 0.7552 (tp) REVERT: A 574 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.4784 (mp) REVERT: A 578 MET cc_start: 0.8330 (mmt) cc_final: 0.7526 (mmt) REVERT: A 637 GLN cc_start: 0.8312 (tp40) cc_final: 0.8002 (tt0) REVERT: B 38 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8081 (tt) REVERT: B 62 ASN cc_start: 0.7758 (m110) cc_final: 0.6917 (t0) REVERT: B 71 LYS cc_start: 0.7483 (mtpt) cc_final: 0.7066 (mmpt) REVERT: B 91 ASN cc_start: 0.7962 (m110) cc_final: 0.7636 (m-40) REVERT: B 99 MET cc_start: 0.8026 (mmm) cc_final: 0.7758 (mmm) REVERT: B 144 SER cc_start: 0.8405 (m) cc_final: 0.7773 (p) REVERT: B 214 GLN cc_start: 0.8282 (mt0) cc_final: 0.7579 (tm-30) REVERT: B 239 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: B 250 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8197 (tp30) REVERT: B 282 GLU cc_start: 0.8137 (tp30) cc_final: 0.7855 (tp30) REVERT: B 294 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7206 (tt0) REVERT: B 300 LYS cc_start: 0.8362 (pmtt) cc_final: 0.7882 (ttmt) REVERT: B 303 GLU cc_start: 0.8490 (tt0) cc_final: 0.8021 (tt0) REVERT: B 401 LEU cc_start: 0.8446 (mt) cc_final: 0.8090 (tt) REVERT: B 440 MET cc_start: 0.8570 (ttp) cc_final: 0.7609 (tpt) REVERT: B 454 MET cc_start: 0.8345 (tpp) cc_final: 0.7943 (tpt) REVERT: B 464 ASN cc_start: 0.7779 (t0) cc_final: 0.7288 (t0) REVERT: B 540 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8162 (mt) REVERT: B 542 ASP cc_start: 0.8002 (m-30) cc_final: 0.7589 (m-30) REVERT: B 574 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4611 (mp) REVERT: B 637 GLN cc_start: 0.8310 (tp40) cc_final: 0.8070 (tt0) REVERT: C 62 ASN cc_start: 0.7820 (m110) cc_final: 0.7003 (t0) REVERT: C 71 LYS cc_start: 0.7337 (mttt) cc_final: 0.6690 (mmpt) REVERT: C 99 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7190 (tmm) REVERT: C 100 GLU cc_start: 0.8597 (tp30) cc_final: 0.8184 (mt-10) REVERT: C 180 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8184 (ttm110) REVERT: C 214 GLN cc_start: 0.8366 (mt0) cc_final: 0.7557 (tm-30) REVERT: C 215 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8765 (ttt) REVERT: C 216 TYR cc_start: 0.9051 (t80) cc_final: 0.8778 (t80) REVERT: C 239 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: C 250 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8009 (tp30) REVERT: C 262 LYS cc_start: 0.8597 (tmtt) cc_final: 0.8200 (tptt) REVERT: C 268 TRP cc_start: 0.8204 (p-90) cc_final: 0.7897 (p-90) REVERT: C 294 GLU cc_start: 0.7998 (tp30) cc_final: 0.7735 (tt0) REVERT: C 300 LYS cc_start: 0.8318 (pmtt) cc_final: 0.7723 (ttmt) REVERT: C 410 MET cc_start: 0.6795 (tmm) cc_final: 0.6556 (tmm) REVERT: C 440 MET cc_start: 0.8531 (ttp) cc_final: 0.7415 (tpt) REVERT: C 481 MET cc_start: 0.7650 (tpp) cc_final: 0.7346 (tpt) REVERT: C 542 ASP cc_start: 0.7830 (m-30) cc_final: 0.7490 (m-30) REVERT: C 637 GLN cc_start: 0.8242 (tp40) cc_final: 0.7941 (tt0) REVERT: D 84 HIS cc_start: 0.7947 (m90) cc_final: 0.7497 (m90) REVERT: D 91 ASN cc_start: 0.7891 (m110) cc_final: 0.7469 (m-40) REVERT: D 144 SER cc_start: 0.8430 (m) cc_final: 0.7782 (p) REVERT: D 214 GLN cc_start: 0.8364 (mt0) cc_final: 0.7605 (tm-30) REVERT: D 215 MET cc_start: 0.8773 (ttt) cc_final: 0.8500 (ttt) REVERT: D 239 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: D 250 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8191 (tp30) REVERT: D 262 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8556 (tptt) REVERT: D 282 GLU cc_start: 0.8257 (tp30) cc_final: 0.7961 (tp30) REVERT: D 303 GLU cc_start: 0.8430 (tt0) cc_final: 0.7974 (tt0) REVERT: D 401 LEU cc_start: 0.8479 (mt) cc_final: 0.8073 (tt) REVERT: D 440 MET cc_start: 0.8521 (ttp) cc_final: 0.7468 (tpt) REVERT: D 454 MET cc_start: 0.8232 (tpp) cc_final: 0.7788 (tpt) REVERT: D 540 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (mt) REVERT: D 564 ILE cc_start: 0.7864 (tp) cc_final: 0.7638 (tp) REVERT: D 574 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.4537 (mp) REVERT: D 637 GLN cc_start: 0.8313 (tp40) cc_final: 0.8045 (tt0) outliers start: 97 outliers final: 47 residues processed: 502 average time/residue: 0.2956 time to fit residues: 230.0246 Evaluate side-chains 464 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 403 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 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: 0.7217 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20266 Z= 0.167 Angle : 0.600 8.143 27518 Z= 0.293 Chirality : 0.040 0.156 3110 Planarity : 0.004 0.050 3458 Dihedral : 6.006 46.575 2879 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.53 % Allowed : 19.73 % Favored : 76.74 % 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: 2440 helix: -0.56 (0.15), residues: 1260 sheet: -2.07 (0.67), residues: 56 loop : -2.65 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 629 HIS 0.004 0.001 HIS B 522 PHE 0.011 0.001 PHE D 415 TYR 0.022 0.001 TYR D 324 ARG 0.006 0.000 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 437 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7749 (m110) cc_final: 0.6858 (t0) REVERT: A 71 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7027 (mmpt) REVERT: A 91 ASN cc_start: 0.7864 (m110) cc_final: 0.7553 (m-40) REVERT: A 99 MET cc_start: 0.7942 (mmm) cc_final: 0.7636 (mmm) REVERT: A 144 SER cc_start: 0.8378 (m) cc_final: 0.7779 (p) REVERT: A 214 GLN cc_start: 0.8185 (mt0) cc_final: 0.7271 (tm-30) REVERT: A 215 MET cc_start: 0.8729 (ttt) cc_final: 0.8507 (ttt) REVERT: A 239 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 250 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8254 (tp30) REVERT: A 262 LYS cc_start: 0.8751 (tmtt) cc_final: 0.8433 (tptt) REVERT: A 282 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 294 GLU cc_start: 0.7921 (tp30) cc_final: 0.7520 (tt0) REVERT: A 300 LYS cc_start: 0.8341 (pmtt) cc_final: 0.7864 (ttmt) REVERT: A 303 GLU cc_start: 0.8341 (tt0) cc_final: 0.8077 (tt0) REVERT: A 306 GLN cc_start: 0.8394 (mt0) cc_final: 0.8134 (tt0) REVERT: A 355 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6167 (ptm-80) REVERT: A 378 MET cc_start: 0.7905 (ttm) cc_final: 0.7280 (ttt) REVERT: A 401 LEU cc_start: 0.8376 (mt) cc_final: 0.8011 (tt) REVERT: A 440 MET cc_start: 0.8387 (ttp) cc_final: 0.7479 (tpt) REVERT: A 454 MET cc_start: 0.8114 (tpp) cc_final: 0.7830 (tpt) REVERT: A 485 MET cc_start: 0.8579 (tpp) cc_final: 0.8354 (tpp) REVERT: A 490 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6662 (tt) REVERT: A 574 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.4650 (mp) REVERT: A 578 MET cc_start: 0.8244 (mmt) cc_final: 0.7727 (mmt) REVERT: A 637 GLN cc_start: 0.8228 (tp40) cc_final: 0.7931 (tt0) REVERT: B 62 ASN cc_start: 0.7755 (m110) cc_final: 0.6924 (t0) REVERT: B 71 LYS cc_start: 0.7437 (mtpt) cc_final: 0.7023 (mmpt) REVERT: B 91 ASN cc_start: 0.7937 (m110) cc_final: 0.7623 (m-40) REVERT: B 99 MET cc_start: 0.7974 (mmm) cc_final: 0.7722 (mmm) REVERT: B 144 SER cc_start: 0.8372 (m) cc_final: 0.7701 (p) REVERT: B 164 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: B 180 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8072 (ttm110) REVERT: B 214 GLN cc_start: 0.8101 (mt0) cc_final: 0.7154 (tm-30) REVERT: B 239 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: B 250 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8236 (tp30) REVERT: B 282 GLU cc_start: 0.8147 (tp30) cc_final: 0.7867 (tp30) REVERT: B 294 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7167 (tt0) REVERT: B 300 LYS cc_start: 0.8363 (pmtt) cc_final: 0.7869 (ttmt) REVERT: B 401 LEU cc_start: 0.8456 (mt) cc_final: 0.8162 (tt) REVERT: B 440 MET cc_start: 0.8417 (ttp) cc_final: 0.7528 (tpt) REVERT: B 454 MET cc_start: 0.8397 (tpp) cc_final: 0.8017 (tpt) REVERT: B 464 ASN cc_start: 0.7642 (t0) cc_final: 0.7299 (t0) REVERT: B 540 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 542 ASP cc_start: 0.7983 (m-30) cc_final: 0.7589 (m-30) REVERT: B 577 MET cc_start: 0.6907 (ttm) cc_final: 0.6627 (ttm) REVERT: B 637 GLN cc_start: 0.8279 (tp40) cc_final: 0.8059 (tt0) REVERT: C 62 ASN cc_start: 0.7822 (m110) cc_final: 0.7046 (t0) REVERT: C 71 LYS cc_start: 0.7251 (mttt) cc_final: 0.6674 (mmpt) REVERT: C 99 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7248 (tmm) REVERT: C 180 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8208 (ttm110) REVERT: C 214 GLN cc_start: 0.8345 (mt0) cc_final: 0.7516 (tm-30) REVERT: C 215 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8647 (ttt) REVERT: C 216 TYR cc_start: 0.9009 (t80) cc_final: 0.8772 (t80) REVERT: C 239 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: C 250 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8018 (tp30) REVERT: C 262 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8171 (tptt) REVERT: C 268 TRP cc_start: 0.8215 (p-90) cc_final: 0.7912 (p-90) REVERT: C 294 GLU cc_start: 0.8035 (tp30) cc_final: 0.7747 (tt0) REVERT: C 300 LYS cc_start: 0.8308 (pmtt) cc_final: 0.7678 (ttmt) REVERT: C 345 MET cc_start: 0.4638 (tmt) cc_final: 0.4314 (tmm) REVERT: C 410 MET cc_start: 0.7042 (tmm) cc_final: 0.6573 (tmm) REVERT: C 440 MET cc_start: 0.8472 (ttp) cc_final: 0.7357 (tpt) REVERT: C 481 MET cc_start: 0.7380 (tpp) cc_final: 0.7123 (tpt) REVERT: C 542 ASP cc_start: 0.7846 (m-30) cc_final: 0.7500 (m-30) REVERT: C 574 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4513 (mp) REVERT: C 615 ARG cc_start: 0.7479 (ttm170) cc_final: 0.6952 (ttm170) REVERT: C 629 TRP cc_start: 0.6767 (m-10) cc_final: 0.5910 (m-10) REVERT: C 634 GLU cc_start: 0.8519 (pm20) cc_final: 0.7628 (mp0) REVERT: C 637 GLN cc_start: 0.8216 (tp40) cc_final: 0.7932 (tt0) REVERT: D 84 HIS cc_start: 0.7945 (m90) cc_final: 0.7497 (m90) REVERT: D 91 ASN cc_start: 0.7887 (m110) cc_final: 0.7540 (m-40) REVERT: D 144 SER cc_start: 0.8389 (m) cc_final: 0.7707 (p) REVERT: D 180 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8070 (ttm110) REVERT: D 214 GLN cc_start: 0.8362 (mt0) cc_final: 0.7646 (tm-30) REVERT: D 215 MET cc_start: 0.8749 (ttt) cc_final: 0.8522 (ttt) REVERT: D 239 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: D 250 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8182 (tp30) REVERT: D 262 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8328 (tptt) REVERT: D 282 GLU cc_start: 0.8229 (tp30) cc_final: 0.7887 (tp30) REVERT: D 303 GLU cc_start: 0.8436 (tt0) cc_final: 0.7970 (tt0) REVERT: D 378 MET cc_start: 0.7981 (ttm) cc_final: 0.7485 (ttt) REVERT: D 440 MET cc_start: 0.8451 (ttp) cc_final: 0.7389 (tpt) REVERT: D 454 MET cc_start: 0.8192 (tpp) cc_final: 0.7895 (tpt) REVERT: D 490 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6209 (tt) REVERT: D 540 ILE cc_start: 0.8312 (mt) cc_final: 0.8104 (mt) REVERT: D 574 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.4917 (mt) REVERT: D 577 MET cc_start: 0.7768 (mtm) cc_final: 0.7496 (ttm) REVERT: D 578 MET cc_start: 0.8423 (mmt) cc_final: 0.7647 (mmt) REVERT: D 637 GLN cc_start: 0.8301 (tp40) cc_final: 0.8037 (tt0) outliers start: 75 outliers final: 38 residues processed: 484 average time/residue: 0.2992 time to fit residues: 225.5465 Evaluate side-chains 456 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 404 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20266 Z= 0.253 Angle : 0.656 9.539 27518 Z= 0.318 Chirality : 0.042 0.140 3110 Planarity : 0.004 0.047 3458 Dihedral : 6.165 52.234 2879 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.47 % Allowed : 19.77 % Favored : 75.75 % 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: -2.17 (0.17), residues: 2440 helix: -0.43 (0.15), residues: 1264 sheet: -2.13 (0.66), residues: 56 loop : -2.64 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 629 HIS 0.005 0.001 HIS B 522 PHE 0.017 0.001 PHE B 415 TYR 0.023 0.002 TYR D 324 ARG 0.006 0.000 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 420 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7832 (m110) cc_final: 0.6993 (t0) REVERT: A 71 LYS cc_start: 0.7435 (mtpt) cc_final: 0.7035 (mmpt) REVERT: A 84 HIS cc_start: 0.7877 (m90) cc_final: 0.7472 (m90) REVERT: A 91 ASN cc_start: 0.7928 (m110) cc_final: 0.7622 (m-40) REVERT: A 99 MET cc_start: 0.7922 (mmm) cc_final: 0.7648 (mmm) REVERT: A 144 SER cc_start: 0.8399 (m) cc_final: 0.7798 (p) REVERT: A 214 GLN cc_start: 0.8256 (mt0) cc_final: 0.7450 (tm-30) REVERT: A 239 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: A 262 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8415 (tptt) REVERT: A 282 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7740 (mt-10) REVERT: A 294 GLU cc_start: 0.8081 (tp30) cc_final: 0.7550 (tt0) REVERT: A 300 LYS cc_start: 0.8376 (pmtt) cc_final: 0.7822 (ttmt) REVERT: A 303 GLU cc_start: 0.8353 (tt0) cc_final: 0.7880 (tt0) REVERT: A 306 GLN cc_start: 0.8429 (mt0) cc_final: 0.8212 (tt0) REVERT: A 355 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6447 (ptm-80) REVERT: A 378 MET cc_start: 0.7980 (ttm) cc_final: 0.7456 (ttt) REVERT: A 401 LEU cc_start: 0.8331 (mt) cc_final: 0.7943 (tt) REVERT: A 440 MET cc_start: 0.8488 (ttp) cc_final: 0.7369 (tpt) REVERT: A 454 MET cc_start: 0.8114 (tpp) cc_final: 0.7765 (tpt) REVERT: A 490 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6587 (tt) REVERT: A 540 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8135 (mt) REVERT: A 564 ILE cc_start: 0.7735 (tp) cc_final: 0.7519 (tp) REVERT: A 574 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.4582 (mp) REVERT: A 637 GLN cc_start: 0.8301 (tp40) cc_final: 0.8037 (tt0) REVERT: B 38 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8123 (tt) REVERT: B 62 ASN cc_start: 0.7800 (m110) cc_final: 0.6950 (t0) REVERT: B 71 LYS cc_start: 0.7407 (mtpt) cc_final: 0.7008 (mmpt) REVERT: B 84 HIS cc_start: 0.7833 (m90) cc_final: 0.7478 (m90) REVERT: B 91 ASN cc_start: 0.7977 (m110) cc_final: 0.7657 (m-40) REVERT: B 144 SER cc_start: 0.8415 (m) cc_final: 0.7772 (p) REVERT: B 180 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8127 (ttm110) REVERT: B 214 GLN cc_start: 0.8074 (mt0) cc_final: 0.7244 (tm-30) REVERT: B 239 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: B 250 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8237 (tp30) REVERT: B 282 GLU cc_start: 0.8151 (tp30) cc_final: 0.7860 (tp30) REVERT: B 294 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7246 (tt0) REVERT: B 300 LYS cc_start: 0.8420 (pmtt) cc_final: 0.7847 (ttmt) REVERT: B 401 LEU cc_start: 0.8415 (mt) cc_final: 0.8048 (tt) REVERT: B 414 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7128 (mmm160) REVERT: B 440 MET cc_start: 0.8511 (ttp) cc_final: 0.7480 (tpt) REVERT: B 454 MET cc_start: 0.8378 (tpp) cc_final: 0.7929 (tpt) REVERT: B 540 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8221 (mt) REVERT: B 541 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8333 (mt) REVERT: B 542 ASP cc_start: 0.7977 (m-30) cc_final: 0.7541 (m-30) REVERT: B 637 GLN cc_start: 0.8290 (tp40) cc_final: 0.8090 (tt0) REVERT: C 62 ASN cc_start: 0.7840 (m110) cc_final: 0.7050 (t0) REVERT: C 71 LYS cc_start: 0.7280 (mttt) cc_final: 0.6721 (mmpt) REVERT: C 99 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7184 (tmm) REVERT: C 180 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8219 (ttm110) REVERT: C 214 GLN cc_start: 0.8371 (mt0) cc_final: 0.7547 (tm-30) REVERT: C 215 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8752 (ttt) REVERT: C 239 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: C 250 GLU cc_start: 0.8851 (mm-30) cc_final: 0.7939 (tp30) REVERT: C 262 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8195 (tptt) REVERT: C 268 TRP cc_start: 0.8193 (p-90) cc_final: 0.7869 (p-90) REVERT: C 294 GLU cc_start: 0.8167 (tp30) cc_final: 0.7828 (tt0) REVERT: C 300 LYS cc_start: 0.8302 (pmtt) cc_final: 0.7414 (tmtt) REVERT: C 440 MET cc_start: 0.8311 (ttp) cc_final: 0.7135 (tpt) REVERT: C 481 MET cc_start: 0.7693 (tpp) cc_final: 0.7436 (tpt) REVERT: C 542 ASP cc_start: 0.7895 (m-30) cc_final: 0.7516 (m-30) REVERT: C 564 ILE cc_start: 0.7694 (tp) cc_final: 0.7468 (tp) REVERT: C 574 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4762 (tp) REVERT: C 637 GLN cc_start: 0.8230 (tp40) cc_final: 0.7968 (tt0) REVERT: D 84 HIS cc_start: 0.7971 (m90) cc_final: 0.7521 (m90) REVERT: D 91 ASN cc_start: 0.7961 (m110) cc_final: 0.7474 (m-40) REVERT: D 99 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7756 (tmm) REVERT: D 144 SER cc_start: 0.8392 (m) cc_final: 0.7736 (p) REVERT: D 180 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8377 (ttm170) REVERT: D 214 GLN cc_start: 0.8414 (mt0) cc_final: 0.7776 (tm-30) REVERT: D 215 MET cc_start: 0.8861 (ttt) cc_final: 0.8647 (ttt) REVERT: D 239 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: D 250 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8163 (tp30) REVERT: D 262 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8298 (tptt) REVERT: D 282 GLU cc_start: 0.8204 (tp30) cc_final: 0.7904 (tp30) REVERT: D 303 GLU cc_start: 0.8438 (tt0) cc_final: 0.7970 (tt0) REVERT: D 378 MET cc_start: 0.8087 (ttm) cc_final: 0.7702 (ttt) REVERT: D 414 ARG cc_start: 0.7464 (mmt-90) cc_final: 0.7225 (mtt-85) REVERT: D 440 MET cc_start: 0.8451 (ttp) cc_final: 0.7301 (tpt) REVERT: D 454 MET cc_start: 0.8213 (tpp) cc_final: 0.7817 (tpt) REVERT: D 490 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6259 (tt) REVERT: D 564 ILE cc_start: 0.7835 (tp) cc_final: 0.7612 (tp) REVERT: D 574 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.4903 (mt) REVERT: D 577 MET cc_start: 0.7820 (mtm) cc_final: 0.7569 (ttp) REVERT: D 637 GLN cc_start: 0.8349 (tp40) cc_final: 0.8091 (tt0) outliers start: 95 outliers final: 53 residues processed: 480 average time/residue: 0.2782 time to fit residues: 209.5673 Evaluate side-chains 468 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 398 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 149 optimal weight: 0.1980 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20266 Z= 0.144 Angle : 0.605 8.555 27518 Z= 0.292 Chirality : 0.039 0.145 3110 Planarity : 0.004 0.045 3458 Dihedral : 5.676 47.522 2879 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.11 % Allowed : 21.23 % Favored : 75.66 % 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: -1.87 (0.17), residues: 2440 helix: -0.12 (0.15), residues: 1256 sheet: -1.95 (0.66), residues: 56 loop : -2.57 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 629 HIS 0.004 0.001 HIS B 522 PHE 0.026 0.001 PHE C 415 TYR 0.021 0.001 TYR B 524 ARG 0.006 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 432 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7877 (m110) cc_final: 0.7019 (t0) REVERT: A 71 LYS cc_start: 0.7458 (mtpt) cc_final: 0.6997 (mmpt) REVERT: A 84 HIS cc_start: 0.7911 (m90) cc_final: 0.7627 (m90) REVERT: A 91 ASN cc_start: 0.7820 (m110) cc_final: 0.7519 (m-40) REVERT: A 99 MET cc_start: 0.7884 (mmm) cc_final: 0.7606 (mmm) REVERT: A 144 SER cc_start: 0.8341 (m) cc_final: 0.7719 (p) REVERT: A 153 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7448 (mtt90) REVERT: A 214 GLN cc_start: 0.8171 (mt0) cc_final: 0.7263 (tm-30) REVERT: A 215 MET cc_start: 0.8619 (ttt) cc_final: 0.8387 (ttt) REVERT: A 239 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: A 262 LYS cc_start: 0.8637 (tmtt) cc_final: 0.8260 (tptt) REVERT: A 282 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 294 GLU cc_start: 0.8030 (tp30) cc_final: 0.7551 (tt0) REVERT: A 300 LYS cc_start: 0.8377 (pmtt) cc_final: 0.7805 (ttmt) REVERT: A 303 GLU cc_start: 0.8337 (tt0) cc_final: 0.8058 (tt0) REVERT: A 315 GLU cc_start: 0.7907 (tp30) cc_final: 0.7518 (mm-30) REVERT: A 355 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6155 (ptm-80) REVERT: A 401 LEU cc_start: 0.8361 (mt) cc_final: 0.7992 (tt) REVERT: A 414 ARG cc_start: 0.7202 (mmt-90) cc_final: 0.6892 (tpp80) REVERT: A 440 MET cc_start: 0.8364 (ttp) cc_final: 0.7228 (tpt) REVERT: A 454 MET cc_start: 0.8137 (tpp) cc_final: 0.7693 (tpt) REVERT: A 490 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6575 (tt) REVERT: A 559 TYR cc_start: 0.8236 (t80) cc_final: 0.8015 (t80) REVERT: A 574 LEU cc_start: 0.5303 (OUTLIER) cc_final: 0.4667 (mp) REVERT: A 578 MET cc_start: 0.8187 (mmt) cc_final: 0.7609 (mmt) REVERT: A 637 GLN cc_start: 0.8310 (tp40) cc_final: 0.8003 (tt0) REVERT: B 62 ASN cc_start: 0.7763 (m110) cc_final: 0.6917 (t0) REVERT: B 71 LYS cc_start: 0.7311 (mtpt) cc_final: 0.6953 (mmpt) REVERT: B 84 HIS cc_start: 0.7787 (m90) cc_final: 0.7464 (m90) REVERT: B 91 ASN cc_start: 0.7909 (m110) cc_final: 0.7580 (m-40) REVERT: B 144 SER cc_start: 0.8286 (m) cc_final: 0.7656 (p) REVERT: B 180 ARG cc_start: 0.8630 (mtm-85) cc_final: 0.8322 (ttm-80) REVERT: B 239 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 250 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8250 (tp30) REVERT: B 282 GLU cc_start: 0.8096 (tp30) cc_final: 0.7825 (tp30) REVERT: B 294 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7166 (tt0) REVERT: B 300 LYS cc_start: 0.8393 (pmtt) cc_final: 0.7802 (ttmt) REVERT: B 315 GLU cc_start: 0.7956 (tp30) cc_final: 0.7508 (mm-30) REVERT: B 324 TYR cc_start: 0.7190 (m-80) cc_final: 0.6942 (m-80) REVERT: B 355 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6664 (ttm170) REVERT: B 401 LEU cc_start: 0.8456 (mt) cc_final: 0.8141 (tt) REVERT: B 414 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7248 (mmm160) REVERT: B 440 MET cc_start: 0.8383 (ttp) cc_final: 0.7373 (tpt) REVERT: B 464 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7607 (t0) REVERT: B 540 ILE cc_start: 0.8415 (mt) cc_final: 0.8104 (mt) REVERT: B 542 ASP cc_start: 0.7931 (m-30) cc_final: 0.7526 (m-30) REVERT: B 577 MET cc_start: 0.6953 (ttm) cc_final: 0.6131 (ttt) REVERT: B 637 GLN cc_start: 0.8322 (tp40) cc_final: 0.8100 (tt0) REVERT: C 62 ASN cc_start: 0.7923 (m110) cc_final: 0.7183 (t0) REVERT: C 71 LYS cc_start: 0.7288 (mttt) cc_final: 0.6765 (mmpt) REVERT: C 180 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8261 (ttm110) REVERT: C 214 GLN cc_start: 0.8260 (mt0) cc_final: 0.7420 (tm-30) REVERT: C 215 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8584 (ttt) REVERT: C 239 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: C 250 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8046 (tp30) REVERT: C 262 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8150 (tptt) REVERT: C 268 TRP cc_start: 0.8185 (p-90) cc_final: 0.7876 (p-90) REVERT: C 294 GLU cc_start: 0.8009 (tp30) cc_final: 0.7759 (tt0) REVERT: C 300 LYS cc_start: 0.8282 (pmtt) cc_final: 0.7409 (tmtt) REVERT: C 324 TYR cc_start: 0.7228 (m-80) cc_final: 0.7006 (m-80) REVERT: C 373 LEU cc_start: 0.7660 (tp) cc_final: 0.7445 (pt) REVERT: C 378 MET cc_start: 0.8316 (ttt) cc_final: 0.7994 (ttm) REVERT: C 414 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7110 (mmm160) REVERT: C 440 MET cc_start: 0.8234 (ttp) cc_final: 0.6989 (tpt) REVERT: C 481 MET cc_start: 0.7514 (tpp) cc_final: 0.7266 (tpt) REVERT: C 542 ASP cc_start: 0.7920 (m-30) cc_final: 0.7551 (m-30) REVERT: C 574 LEU cc_start: 0.5092 (OUTLIER) cc_final: 0.4699 (tp) REVERT: C 634 GLU cc_start: 0.8420 (pm20) cc_final: 0.7661 (mp0) REVERT: C 637 GLN cc_start: 0.8222 (tp40) cc_final: 0.7940 (tt0) REVERT: D 84 HIS cc_start: 0.7900 (m90) cc_final: 0.7476 (m90) REVERT: D 91 ASN cc_start: 0.7846 (m110) cc_final: 0.7503 (m-40) REVERT: D 99 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: D 144 SER cc_start: 0.8357 (m) cc_final: 0.7633 (p) REVERT: D 180 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8315 (ttm-80) REVERT: D 214 GLN cc_start: 0.8384 (mt0) cc_final: 0.7653 (tm-30) REVERT: D 215 MET cc_start: 0.8742 (ttt) cc_final: 0.8500 (ttt) REVERT: D 239 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: D 250 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8153 (tp30) REVERT: D 262 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8251 (tptt) REVERT: D 294 GLU cc_start: 0.7064 (tt0) cc_final: 0.6717 (tt0) REVERT: D 414 ARG cc_start: 0.7458 (mmt-90) cc_final: 0.7219 (mtt-85) REVERT: D 440 MET cc_start: 0.8263 (ttp) cc_final: 0.7347 (tpp) REVERT: D 454 MET cc_start: 0.8152 (tpp) cc_final: 0.7904 (tpt) REVERT: D 464 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7627 (t0) REVERT: D 485 MET cc_start: 0.8787 (tpp) cc_final: 0.8392 (tpp) REVERT: D 490 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6127 (tt) REVERT: D 574 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4870 (mt) REVERT: D 577 MET cc_start: 0.7779 (mtm) cc_final: 0.7500 (ttm) REVERT: D 578 MET cc_start: 0.8392 (mmt) cc_final: 0.7709 (mmt) REVERT: D 637 GLN cc_start: 0.8313 (tp40) cc_final: 0.8067 (tt0) outliers start: 66 outliers final: 34 residues processed: 475 average time/residue: 0.2830 time to fit residues: 209.4064 Evaluate side-chains 450 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 401 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20266 Z= 0.166 Angle : 0.621 8.226 27518 Z= 0.298 Chirality : 0.040 0.170 3110 Planarity : 0.004 0.043 3458 Dihedral : 5.620 47.924 2879 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.30 % Allowed : 22.03 % Favored : 74.67 % 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: -1.75 (0.17), residues: 2440 helix: -0.02 (0.15), residues: 1260 sheet: -1.97 (0.66), residues: 56 loop : -2.51 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP B 629 HIS 0.004 0.001 HIS B 522 PHE 0.019 0.001 PHE B 415 TYR 0.021 0.001 TYR B 623 ARG 0.006 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 417 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7886 (m110) cc_final: 0.7019 (t0) REVERT: A 71 LYS cc_start: 0.7346 (mtpt) cc_final: 0.6961 (mmpt) REVERT: A 84 HIS cc_start: 0.7874 (m90) cc_final: 0.7671 (m90) REVERT: A 91 ASN cc_start: 0.7817 (m110) cc_final: 0.7509 (m-40) REVERT: A 99 MET cc_start: 0.7852 (mmm) cc_final: 0.7584 (mmm) REVERT: A 153 ARG cc_start: 0.7711 (mtt90) cc_final: 0.7471 (mtt90) REVERT: A 214 GLN cc_start: 0.8191 (mt0) cc_final: 0.7470 (tm-30) REVERT: A 239 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: A 262 LYS cc_start: 0.8626 (tmtt) cc_final: 0.8255 (tptt) REVERT: A 282 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 294 GLU cc_start: 0.8076 (tp30) cc_final: 0.7453 (tt0) REVERT: A 303 GLU cc_start: 0.8304 (tt0) cc_final: 0.8006 (tt0) REVERT: A 315 GLU cc_start: 0.7918 (tp30) cc_final: 0.7546 (mm-30) REVERT: A 355 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6250 (ptm-80) REVERT: A 401 LEU cc_start: 0.8355 (mt) cc_final: 0.7974 (tt) REVERT: A 440 MET cc_start: 0.8297 (ttp) cc_final: 0.7113 (tpt) REVERT: A 454 MET cc_start: 0.8133 (tpp) cc_final: 0.7720 (tpt) REVERT: A 485 MET cc_start: 0.8334 (tpp) cc_final: 0.7138 (ttt) REVERT: A 490 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6608 (tt) REVERT: A 574 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4540 (tp) REVERT: A 578 MET cc_start: 0.8190 (mmt) cc_final: 0.7596 (mmt) REVERT: A 637 GLN cc_start: 0.8307 (tp40) cc_final: 0.8007 (tt0) REVERT: B 62 ASN cc_start: 0.7713 (m110) cc_final: 0.6921 (t0) REVERT: B 71 LYS cc_start: 0.7280 (mtpt) cc_final: 0.6949 (mmpt) REVERT: B 91 ASN cc_start: 0.7905 (m110) cc_final: 0.7572 (m-40) REVERT: B 99 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6473 (tmm) REVERT: B 139 ARG cc_start: 0.7492 (tpp80) cc_final: 0.6828 (mtt90) REVERT: B 144 SER cc_start: 0.8372 (m) cc_final: 0.7691 (p) REVERT: B 180 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8227 (ttm-80) REVERT: B 239 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: B 250 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8199 (tp30) REVERT: B 282 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: B 294 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7137 (tt0) REVERT: B 300 LYS cc_start: 0.8395 (pmtt) cc_final: 0.7788 (ttmt) REVERT: B 315 GLU cc_start: 0.7945 (tp30) cc_final: 0.7516 (mm-30) REVERT: B 324 TYR cc_start: 0.7224 (m-80) cc_final: 0.6990 (m-80) REVERT: B 355 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6677 (ttm170) REVERT: B 414 ARG cc_start: 0.7775 (tpp80) cc_final: 0.7108 (mmm160) REVERT: B 440 MET cc_start: 0.8405 (ttp) cc_final: 0.7364 (tpt) REVERT: B 464 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7601 (t0) REVERT: B 540 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (mt) REVERT: B 542 ASP cc_start: 0.7955 (m-30) cc_final: 0.7511 (m-30) REVERT: B 637 GLN cc_start: 0.8326 (tp40) cc_final: 0.8078 (tt0) REVERT: C 62 ASN cc_start: 0.7921 (m110) cc_final: 0.7182 (t0) REVERT: C 71 LYS cc_start: 0.7289 (mttt) cc_final: 0.6762 (mmpt) REVERT: C 180 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8269 (ttm110) REVERT: C 214 GLN cc_start: 0.8271 (mt0) cc_final: 0.7431 (tm-30) REVERT: C 215 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8592 (ttt) REVERT: C 239 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: C 250 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8018 (tp30) REVERT: C 262 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8144 (tptt) REVERT: C 268 TRP cc_start: 0.8187 (p-90) cc_final: 0.7866 (p-90) REVERT: C 282 GLU cc_start: 0.8123 (tp30) cc_final: 0.7861 (tp30) REVERT: C 294 GLU cc_start: 0.8060 (tp30) cc_final: 0.7797 (tt0) REVERT: C 300 LYS cc_start: 0.8294 (pmtt) cc_final: 0.7430 (tmtt) REVERT: C 373 LEU cc_start: 0.7624 (tp) cc_final: 0.7421 (pt) REVERT: C 378 MET cc_start: 0.8387 (ttt) cc_final: 0.8067 (ttm) REVERT: C 414 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7156 (mmm160) REVERT: C 440 MET cc_start: 0.8208 (ttp) cc_final: 0.6945 (tpt) REVERT: C 481 MET cc_start: 0.7644 (tpp) cc_final: 0.7418 (tpt) REVERT: C 542 ASP cc_start: 0.7841 (m-30) cc_final: 0.7461 (m-30) REVERT: C 574 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4642 (tp) REVERT: C 577 MET cc_start: 0.6929 (ttp) cc_final: 0.6631 (ttm) REVERT: C 634 GLU cc_start: 0.8405 (pm20) cc_final: 0.7662 (mp0) REVERT: C 637 GLN cc_start: 0.8263 (tp40) cc_final: 0.7977 (tt0) REVERT: D 71 LYS cc_start: 0.7184 (tttt) cc_final: 0.6764 (tptt) REVERT: D 84 HIS cc_start: 0.7933 (m90) cc_final: 0.7519 (m90) REVERT: D 91 ASN cc_start: 0.7855 (m110) cc_final: 0.7510 (m-40) REVERT: D 180 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8260 (ttm-80) REVERT: D 214 GLN cc_start: 0.8392 (mt0) cc_final: 0.7632 (tm-30) REVERT: D 215 MET cc_start: 0.8739 (ttt) cc_final: 0.8502 (ttt) REVERT: D 239 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: D 250 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8208 (tp30) REVERT: D 262 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8251 (tptt) REVERT: D 294 GLU cc_start: 0.7022 (tt0) cc_final: 0.6678 (tt0) REVERT: D 414 ARG cc_start: 0.7420 (mmt-90) cc_final: 0.7173 (mtt-85) REVERT: D 440 MET cc_start: 0.8223 (ttp) cc_final: 0.7308 (tpp) REVERT: D 454 MET cc_start: 0.8196 (tpp) cc_final: 0.7935 (tpt) REVERT: D 464 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7633 (t0) REVERT: D 485 MET cc_start: 0.8748 (tpp) cc_final: 0.8450 (tpp) REVERT: D 490 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6012 (tt) REVERT: D 574 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4758 (tp) REVERT: D 577 MET cc_start: 0.7853 (mtm) cc_final: 0.7586 (ttm) REVERT: D 578 MET cc_start: 0.8370 (mmt) cc_final: 0.7725 (mmt) REVERT: D 637 GLN cc_start: 0.8310 (tp40) cc_final: 0.8066 (tt0) outliers start: 70 outliers final: 40 residues processed: 457 average time/residue: 0.2865 time to fit residues: 204.2073 Evaluate side-chains 456 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 399 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.7980 chunk 231 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20266 Z= 0.199 Angle : 0.639 8.598 27518 Z= 0.308 Chirality : 0.041 0.165 3110 Planarity : 0.004 0.041 3458 Dihedral : 5.693 49.823 2879 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.01 % Allowed : 22.79 % Favored : 74.20 % 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: -1.74 (0.17), residues: 2440 helix: -0.01 (0.15), residues: 1272 sheet: -2.01 (0.66), residues: 56 loop : -2.55 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 629 HIS 0.007 0.001 HIS D 522 PHE 0.023 0.001 PHE C 415 TYR 0.021 0.001 TYR B 623 ARG 0.006 0.000 ARG B 615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 401 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7765 (m110) cc_final: 0.6933 (t0) REVERT: A 71 LYS cc_start: 0.7388 (mtpt) cc_final: 0.6991 (mmpt) REVERT: A 84 HIS cc_start: 0.7925 (m90) cc_final: 0.7575 (m90) REVERT: A 91 ASN cc_start: 0.7832 (m110) cc_final: 0.7518 (m-40) REVERT: A 99 MET cc_start: 0.7897 (mmm) cc_final: 0.7643 (mmm) REVERT: A 153 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7467 (mtt90) REVERT: A 214 GLN cc_start: 0.7959 (mt0) cc_final: 0.7180 (tm-30) REVERT: A 239 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 262 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8261 (tptt) REVERT: A 282 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 294 GLU cc_start: 0.8078 (tp30) cc_final: 0.7579 (tt0) REVERT: A 303 GLU cc_start: 0.8285 (tt0) cc_final: 0.7789 (tt0) REVERT: A 315 GLU cc_start: 0.7899 (tp30) cc_final: 0.7529 (mm-30) REVERT: A 355 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6390 (ptm-80) REVERT: A 401 LEU cc_start: 0.8369 (mt) cc_final: 0.7960 (tt) REVERT: A 410 MET cc_start: 0.7091 (tmm) cc_final: 0.6428 (tmm) REVERT: A 414 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.6977 (tpp80) REVERT: A 440 MET cc_start: 0.8248 (ttp) cc_final: 0.7054 (tpt) REVERT: A 454 MET cc_start: 0.8159 (tpp) cc_final: 0.7706 (tpt) REVERT: A 485 MET cc_start: 0.8310 (tpp) cc_final: 0.7546 (ttm) REVERT: A 490 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6607 (tt) REVERT: A 574 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4650 (tp) REVERT: A 578 MET cc_start: 0.8090 (mmt) cc_final: 0.7516 (mmt) REVERT: A 637 GLN cc_start: 0.8316 (tp40) cc_final: 0.8033 (tt0) REVERT: B 62 ASN cc_start: 0.7764 (m110) cc_final: 0.6919 (t0) REVERT: B 71 LYS cc_start: 0.7283 (mtpt) cc_final: 0.6814 (mmpt) REVERT: B 91 ASN cc_start: 0.7937 (m110) cc_final: 0.7605 (m-40) REVERT: B 99 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6499 (tmm) REVERT: B 139 ARG cc_start: 0.7535 (tpp80) cc_final: 0.6848 (mtt90) REVERT: B 144 SER cc_start: 0.8362 (m) cc_final: 0.7676 (p) REVERT: B 180 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8180 (ttm-80) REVERT: B 184 GLU cc_start: 0.8538 (tt0) cc_final: 0.8175 (mt-10) REVERT: B 214 GLN cc_start: 0.7824 (mt0) cc_final: 0.7167 (tm-30) REVERT: B 239 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: B 250 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8180 (tp30) REVERT: B 282 GLU cc_start: 0.8163 (tp30) cc_final: 0.7878 (tp30) REVERT: B 294 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7117 (tt0) REVERT: B 315 GLU cc_start: 0.7946 (tp30) cc_final: 0.7560 (tp30) REVERT: B 324 TYR cc_start: 0.7301 (m-80) cc_final: 0.7024 (m-80) REVERT: B 355 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6668 (ttm170) REVERT: B 401 LEU cc_start: 0.8428 (mt) cc_final: 0.8072 (tt) REVERT: B 414 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7098 (mmm160) REVERT: B 440 MET cc_start: 0.8474 (ttp) cc_final: 0.7401 (tpt) REVERT: B 540 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8239 (mt) REVERT: B 542 ASP cc_start: 0.7925 (m-30) cc_final: 0.7468 (m-30) REVERT: B 637 GLN cc_start: 0.8331 (tp40) cc_final: 0.8083 (tt0) REVERT: C 62 ASN cc_start: 0.7917 (m110) cc_final: 0.7155 (t0) REVERT: C 71 LYS cc_start: 0.7292 (mttt) cc_final: 0.6759 (mmpt) REVERT: C 180 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8282 (ttm110) REVERT: C 214 GLN cc_start: 0.8327 (mt0) cc_final: 0.7484 (tm-30) REVERT: C 215 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8623 (ttt) REVERT: C 239 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: C 250 GLU cc_start: 0.8815 (mm-30) cc_final: 0.7995 (tp30) REVERT: C 262 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8194 (tptt) REVERT: C 268 TRP cc_start: 0.8199 (p-90) cc_final: 0.7860 (p-90) REVERT: C 282 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: C 294 GLU cc_start: 0.8052 (tp30) cc_final: 0.7784 (tt0) REVERT: C 300 LYS cc_start: 0.8302 (pmtt) cc_final: 0.7431 (tmtt) REVERT: C 378 MET cc_start: 0.8423 (ttt) cc_final: 0.8113 (ttm) REVERT: C 414 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7113 (mmm160) REVERT: C 440 MET cc_start: 0.8235 (ttp) cc_final: 0.6963 (tpt) REVERT: C 481 MET cc_start: 0.7759 (tpp) cc_final: 0.7519 (tpt) REVERT: C 542 ASP cc_start: 0.7784 (m-30) cc_final: 0.7409 (m-30) REVERT: C 574 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4604 (tp) REVERT: C 634 GLU cc_start: 0.8417 (pm20) cc_final: 0.7610 (mp0) REVERT: C 637 GLN cc_start: 0.8300 (tp40) cc_final: 0.8032 (tt0) REVERT: D 71 LYS cc_start: 0.7217 (tttt) cc_final: 0.6869 (tptt) REVERT: D 84 HIS cc_start: 0.7955 (m90) cc_final: 0.7535 (m90) REVERT: D 91 ASN cc_start: 0.7846 (m110) cc_final: 0.7371 (m-40) REVERT: D 99 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7716 (tmm) REVERT: D 180 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8275 (ttm-80) REVERT: D 214 GLN cc_start: 0.8441 (mt0) cc_final: 0.7681 (tm-30) REVERT: D 239 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: D 250 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8161 (tp30) REVERT: D 262 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8281 (tptt) REVERT: D 294 GLU cc_start: 0.7034 (tt0) cc_final: 0.6694 (tt0) REVERT: D 414 ARG cc_start: 0.7394 (mmt-90) cc_final: 0.7167 (mtt-85) REVERT: D 440 MET cc_start: 0.8248 (ttp) cc_final: 0.7026 (tpt) REVERT: D 454 MET cc_start: 0.8186 (tpp) cc_final: 0.7886 (tpt) REVERT: D 485 MET cc_start: 0.8767 (tpp) cc_final: 0.8335 (tpp) REVERT: D 490 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6124 (tt) REVERT: D 574 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4738 (mt) REVERT: D 577 MET cc_start: 0.7853 (mtm) cc_final: 0.7596 (ttm) REVERT: D 578 MET cc_start: 0.8416 (mmt) cc_final: 0.7512 (mmt) REVERT: D 637 GLN cc_start: 0.8339 (tp40) cc_final: 0.8090 (tt0) outliers start: 64 outliers final: 41 residues processed: 441 average time/residue: 0.2890 time to fit residues: 198.0097 Evaluate side-chains 446 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 389 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140294 restraints weight = 27236.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144289 restraints weight = 15105.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146954 restraints weight = 10175.745| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20266 Z= 0.160 Angle : 0.614 7.854 27518 Z= 0.297 Chirality : 0.040 0.174 3110 Planarity : 0.004 0.041 3458 Dihedral : 5.511 47.534 2879 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.59 % Allowed : 23.45 % Favored : 73.96 % 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: -1.64 (0.17), residues: 2440 helix: 0.11 (0.15), residues: 1272 sheet: -1.89 (0.66), residues: 56 loop : -2.55 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 629 HIS 0.009 0.001 HIS D 522 PHE 0.023 0.001 PHE C 415 TYR 0.022 0.001 TYR C 324 ARG 0.007 0.000 ARG C 615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4578.37 seconds wall clock time: 83 minutes 27.79 seconds (5007.79 seconds total)