Starting phenix.real_space_refine on Fri Nov 17 16:55:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/11_2023/7k4d_22665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/11_2023/7k4d_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_22665/11_2023/7k4d_22665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/11_2023/7k4d_22665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/11_2023/7k4d_22665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4d_22665/11_2023/7k4d_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 10.29, per 1000 atoms: 0.52 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: 7.56 Conformation dependent library (CDL) restraints added in 3.1 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: 3.72 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: 4.88 Time building geometry restraints manager: 8.15 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 - 21.14: 11450 21.14 - 42.28: 583 42.28 - 63.42: 40 63.42 - 84.56: 8 84.56 - 105.70: 2 Dihedral angle restraints: 12083 sinusoidal: 4923 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 12080 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.680 Check model and map are aligned: 0.280 Set scattering table: 0.210 Process input model: 48.760 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.100 ------------------------------------------------------------------------------- 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 : 12.054 105.697 7459 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 *********************** 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 : 2.390 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 636 average time/residue: 0.3349 time to fit residues: 315.8763 Evaluate side-chains 417 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 128 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 596 GLN C 59 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 572 ASN D 596 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20266 Z= 0.229 Angle : 0.704 8.959 27518 Z= 0.361 Chirality : 0.042 0.179 3110 Planarity : 0.006 0.067 3458 Dihedral : 6.600 42.645 2739 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.63 % Allowed : 13.89 % Favored : 82.49 % 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: -4.75 (0.13), residues: 2440 helix: -2.95 (0.11), residues: 1308 sheet: -2.59 (0.62), residues: 56 loop : -3.37 (0.16), residues: 1076 *********************** 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 541 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 464 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 28 residues processed: 514 average time/residue: 0.2874 time to fit residues: 230.6579 Evaluate side-chains 414 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 386 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2305 time to fit residues: 14.2145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.1980 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN B 59 GLN B 128 GLN B 206 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 473 GLN B 572 ASN C 128 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN C 582 HIS ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20266 Z= 0.231 Angle : 0.665 9.678 27518 Z= 0.333 Chirality : 0.041 0.234 3110 Planarity : 0.005 0.055 3458 Dihedral : 6.182 43.528 2739 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.45 % Allowed : 17.66 % Favored : 79.90 % 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: -3.72 (0.15), residues: 2440 helix: -2.01 (0.13), residues: 1312 sheet: -2.42 (0.63), residues: 56 loop : -3.02 (0.18), residues: 1072 *********************** 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 477 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 425 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 14 residues processed: 454 average time/residue: 0.2965 time to fit residues: 211.4460 Evaluate side-chains 411 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 397 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1661 time to fit residues: 7.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 128 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4097 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= 0.162 Angle : 0.619 9.792 27518 Z= 0.305 Chirality : 0.039 0.178 3110 Planarity : 0.004 0.053 3458 Dihedral : 5.786 40.713 2739 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.59 % Allowed : 19.16 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.16), residues: 2440 helix: -1.43 (0.13), residues: 1288 sheet: -2.09 (0.67), residues: 56 loop : -2.75 (0.18), residues: 1096 *********************** 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 483 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 428 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 463 average time/residue: 0.2969 time to fit residues: 215.3315 Evaluate side-chains 411 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 387 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1825 time to fit residues: 11.3830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 128 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20266 Z= 0.258 Angle : 0.666 12.669 27518 Z= 0.326 Chirality : 0.042 0.276 3110 Planarity : 0.004 0.050 3458 Dihedral : 5.981 44.360 2739 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.78 % Allowed : 20.57 % Favored : 76.65 % 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: -2.75 (0.16), residues: 2440 helix: -1.12 (0.14), residues: 1292 sheet: -2.16 (0.67), residues: 56 loop : -2.67 (0.18), residues: 1092 *********************** 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 460 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 401 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 23 residues processed: 441 average time/residue: 0.3029 time to fit residues: 206.4131 Evaluate side-chains 390 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 367 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1990 time to fit residues: 11.0708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 0.3980 chunk 195 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 201 HIS ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 128 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** B 596 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** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20266 Z= 0.164 Angle : 0.613 13.290 27518 Z= 0.297 Chirality : 0.039 0.169 3110 Planarity : 0.004 0.049 3458 Dihedral : 5.603 42.771 2739 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.79 % Allowed : 20.67 % Favored : 77.54 % 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: -2.35 (0.17), residues: 2440 helix: -0.61 (0.15), residues: 1272 sheet: -2.04 (0.68), residues: 56 loop : -2.71 (0.18), residues: 1112 *********************** 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 453 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 10 residues processed: 437 average time/residue: 0.3234 time to fit residues: 221.1060 Evaluate side-chains 375 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 365 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1866 time to fit residues: 6.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 134 optimal weight: 0.4980 chunk 172 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 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** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20266 Z= 0.159 Angle : 0.628 12.634 27518 Z= 0.301 Chirality : 0.040 0.214 3110 Planarity : 0.004 0.048 3458 Dihedral : 5.437 41.332 2739 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.41 % Allowed : 22.41 % Favored : 76.18 % 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: -2.26 (0.17), residues: 2440 helix: -0.48 (0.14), residues: 1300 sheet: -2.02 (0.67), residues: 56 loop : -2.79 (0.18), residues: 1084 *********************** 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 421 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 391 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 408 average time/residue: 0.3179 time to fit residues: 200.4438 Evaluate side-chains 372 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 361 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1839 time to fit residues: 6.8825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.0010 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 0.0770 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 overall best weight: 0.6146 ------------------------------------------------------------------------------- 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 206 GLN C 252 ASN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5175 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= 0.151 Angle : 0.636 11.049 27518 Z= 0.301 Chirality : 0.039 0.170 3110 Planarity : 0.004 0.048 3458 Dihedral : 5.248 39.515 2739 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.99 % Allowed : 23.35 % 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: -2.11 (0.17), residues: 2440 helix: -0.34 (0.15), residues: 1308 sheet: -1.93 (0.67), residues: 56 loop : -2.77 (0.18), residues: 1076 *********************** 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 410 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 389 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 401 average time/residue: 0.3009 time to fit residues: 189.3232 Evaluate side-chains 375 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 364 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1826 time to fit residues: 6.7011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 128 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 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20266 Z= 0.166 Angle : 0.633 11.904 27518 Z= 0.302 Chirality : 0.040 0.154 3110 Planarity : 0.004 0.051 3458 Dihedral : 5.200 40.380 2739 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.66 % Allowed : 24.39 % Favored : 74.95 % 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: -1.85 (0.17), residues: 2440 helix: -0.09 (0.15), residues: 1276 sheet: -1.90 (0.67), residues: 56 loop : -2.62 (0.18), residues: 1108 *********************** 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 401 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 387 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 391 average time/residue: 0.3062 time to fit residues: 189.0444 Evaluate side-chains 373 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 367 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1933 time to fit residues: 5.6286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 0.0970 chunk 243 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 118 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 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 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20266 Z= 0.150 Angle : 0.634 11.835 27518 Z= 0.300 Chirality : 0.039 0.147 3110 Planarity : 0.004 0.050 3458 Dihedral : 5.008 37.146 2739 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.28 % Allowed : 25.00 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2440 helix: 0.10 (0.15), residues: 1280 sheet: -1.82 (0.67), residues: 56 loop : -2.52 (0.18), residues: 1104 ********************** 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 397 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 391 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 392 average time/residue: 0.3272 time to fit residues: 201.0953 Evaluate side-chains 370 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 366 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2318 time to fit residues: 4.8836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 128 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 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** 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 = 0.3993 r_free = 0.3993 target = 0.175527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139271 restraints weight = 27567.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143053 restraints weight = 15905.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145565 restraints weight = 11005.985| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20266 Z= 0.193 Angle : 0.646 13.104 27518 Z= 0.307 Chirality : 0.040 0.148 3110 Planarity : 0.004 0.058 3458 Dihedral : 5.153 41.314 2739 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.38 % Allowed : 25.38 % Favored : 74.25 % 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: -1.56 (0.17), residues: 2440 helix: 0.12 (0.15), residues: 1276 sheet: -1.89 (0.67), residues: 56 loop : -2.44 (0.18), residues: 1108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4483.65 seconds wall clock time: 84 minutes 28.14 seconds (5068.14 seconds total)