Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 07:15:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/10_2023/8p7w_17537.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/10_2023/8p7w_17537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/10_2023/8p7w_17537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/10_2023/8p7w_17537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/10_2023/8p7w_17537.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/10_2023/8p7w_17537.pdb" } resolution = 3.04 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9232 2.51 5 N 2392 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 6": "OE1" <-> "OE2" Residue "Y GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 14380 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4509 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 19, 'TRANS': 559} Chain breaks: 3 Chain: "B" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4509 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 19, 'TRANS': 559} Chain breaks: 3 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Y" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 7.78, per 1000 atoms: 0.54 Number of scatterers: 14380 At special positions: 0 Unit cell: (93.24, 91.56, 183.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2678 8.00 N 2392 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 50 " - pdb=" SG CYS Y 106 " distance=2.03 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: 5.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 38.2% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.906A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.619A pdb=" N PHE A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.518A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.050A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.837A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.651A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.580A pdb=" N LEU A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.556A pdb=" N LEU A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.825A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 removed outlier: 3.898A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.615A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.621A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.724A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 removed outlier: 3.844A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.514A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.699A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.541A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 5.076A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.904A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.617A pdb=" N PHE B 117 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.500A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.534A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 4.036A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 4.098A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.654A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.630A pdb=" N LEU B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.576A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.823A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 413 removed outlier: 3.819A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 removed outlier: 3.595A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 removed outlier: 3.600A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 476 removed outlier: 3.727A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 removed outlier: 3.867A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix Processing helix chain 'B' and resid 502 through 528 removed outlier: 3.684A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.574A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 Processing helix chain 'B' and resid 572 through 586 Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 5.073A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.107A pdb=" N TYR C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.046A pdb=" N TYR Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 71 removed outlier: 5.560A pdb=" N SER A 65 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY A 69 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS A 40 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 71 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER A 38 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.386A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 310 removed outlier: 4.080A pdb=" N ARG A 309 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 71 removed outlier: 5.473A pdb=" N SER B 65 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 44 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY B 69 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS B 40 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET B 71 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER B 38 " --> pdb=" O MET B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.375A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 255 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.813A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.588A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.588A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.458A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.764A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'G' and resid 44 through 48 removed outlier: 6.421A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.845A pdb=" N SER Y 71 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 46 through 49 removed outlier: 7.078A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1746 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: 4.87 Time building geometry restraints manager: 6.04 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: 4530 1.34 - 1.46: 3605 1.46 - 1.58: 6445 1.58 - 1.70: 0 1.70 - 1.81: 118 Bond restraints: 14698 Sorted by residual: bond pdb=" CG PRO D 88 " pdb=" CD PRO D 88 " ideal model delta sigma weight residual 1.503 1.552 -0.049 3.40e-02 8.65e+02 2.04e+00 bond pdb=" C CYS A 592 " pdb=" O CYS A 592 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.87e+00 bond pdb=" C CYS B 592 " pdb=" O CYS B 592 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.81e+00 bond pdb=" CA ARG C 67 " pdb=" CB ARG C 67 " ideal model delta sigma weight residual 1.526 1.546 -0.020 1.51e-02 4.39e+03 1.69e+00 bond pdb=" CG1 ILE B 412 " pdb=" CD1 ILE B 412 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 ... (remaining 14693 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.03: 213 105.03 - 112.28: 7278 112.28 - 119.53: 4861 119.53 - 126.78: 7383 126.78 - 134.02: 181 Bond angle restraints: 19916 Sorted by residual: angle pdb=" N GLU B 458 " pdb=" CA GLU B 458 " pdb=" CB GLU B 458 " ideal model delta sigma weight residual 110.12 115.83 -5.71 1.47e+00 4.63e-01 1.51e+01 angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.42e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" CB MET Y 83 " pdb=" CG MET Y 83 " pdb=" SD MET Y 83 " ideal model delta sigma weight residual 112.70 123.85 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C TYR D 60 " pdb=" N ASN D 61 " pdb=" CA ASN D 61 " ideal model delta sigma weight residual 120.49 125.58 -5.09 1.42e+00 4.96e-01 1.28e+01 ... (remaining 19911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7471 17.71 - 35.42: 950 35.42 - 53.14: 191 53.14 - 70.85: 29 70.85 - 88.56: 16 Dihedral angle restraints: 8657 sinusoidal: 3355 harmonic: 5302 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 138.05 -45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS Y 50 " pdb=" SG CYS Y 50 " pdb=" SG CYS Y 106 " pdb=" CB CYS Y 106 " ideal model delta sinusoidal sigma weight residual 93.00 54.71 38.29 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS C 50 " pdb=" SG CYS C 50 " pdb=" SG CYS C 106 " pdb=" CB CYS C 106 " ideal model delta sinusoidal sigma weight residual 93.00 57.95 35.05 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 8654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1222 0.029 - 0.058: 701 0.058 - 0.087: 216 0.087 - 0.116: 80 0.116 - 0.145: 29 Chirality restraints: 2248 Sorted by residual: chirality pdb=" CA ILE Y 51 " pdb=" N ILE Y 51 " pdb=" C ILE Y 51 " pdb=" CB ILE Y 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA LEU B 140 " pdb=" N LEU B 140 " pdb=" C LEU B 140 " pdb=" CB LEU B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2245 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO D 88 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 90 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ASP F 90 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP F 90 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F 91 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 68 " 0.013 2.00e-02 2.50e+03 1.41e-02 3.46e+00 pdb=" CG PHE C 68 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 68 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 68 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 68 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 68 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 68 " 0.000 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1494 2.74 - 3.28: 13842 3.28 - 3.82: 23824 3.82 - 4.36: 27027 4.36 - 4.90: 48398 Nonbonded interactions: 114585 Sorted by model distance: nonbonded pdb=" OG1 THR D 23 " pdb=" OE1 GLN D 78 " model vdw 2.206 2.440 nonbonded pdb=" O ASN C 103 " pdb=" OH TYR C 109 " model vdw 2.217 2.440 nonbonded pdb=" O LEU C 11 " pdb=" OG1 THR C 121 " model vdw 2.219 2.440 nonbonded pdb=" O SER G 77 " pdb=" OG SER G 77 " model vdw 2.221 2.440 nonbonded pdb=" O ASN Y 103 " pdb=" OH TYR Y 109 " model vdw 2.229 2.440 ... (remaining 114580 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'Y' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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 individual isotropic 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: 6.050 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: 14.480 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 40.050 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.004 0.053 14698 Z= 0.247 Angle : 0.723 11.978 19916 Z= 0.424 Chirality : 0.042 0.145 2248 Planarity : 0.004 0.101 2508 Dihedral : 15.985 88.560 5248 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.45 % Allowed : 23.09 % 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: -1.44 (0.20), residues: 1824 helix: 1.05 (0.21), residues: 652 sheet: -1.48 (0.24), residues: 390 loop : -2.46 (0.20), residues: 782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 382 time to evaluate : 1.854 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 385 average time/residue: 0.2803 time to fit residues: 155.1735 Evaluate side-chains 356 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1217 time to fit residues: 2.4979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 141 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14698 Z= 0.186 Angle : 0.531 7.594 19916 Z= 0.272 Chirality : 0.039 0.136 2248 Planarity : 0.003 0.070 2508 Dihedral : 3.692 20.552 2000 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.07 % Allowed : 20.10 % Favored : 75.83 % 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: -1.08 (0.20), residues: 1824 helix: 1.49 (0.21), residues: 652 sheet: -1.20 (0.26), residues: 392 loop : -2.45 (0.20), residues: 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 378 time to evaluate : 1.601 Fit side-chains outliers start: 64 outliers final: 35 residues processed: 404 average time/residue: 0.2919 time to fit residues: 171.8347 Evaluate side-chains 390 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 355 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2260 time to fit residues: 16.7104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.0770 chunk 50 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 162 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 158 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 158 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN F 16 GLN Y 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14698 Z= 0.189 Angle : 0.519 7.198 19916 Z= 0.265 Chirality : 0.039 0.142 2248 Planarity : 0.003 0.060 2508 Dihedral : 3.643 21.069 2000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.42 % Allowed : 21.06 % Favored : 76.53 % 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: -0.87 (0.20), residues: 1824 helix: 1.66 (0.21), residues: 654 sheet: -1.15 (0.26), residues: 380 loop : -2.29 (0.21), residues: 790 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 369 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 386 average time/residue: 0.2688 time to fit residues: 150.9760 Evaluate side-chains 374 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 355 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1518 time to fit residues: 7.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14698 Z= 0.242 Angle : 0.539 8.005 19916 Z= 0.277 Chirality : 0.040 0.150 2248 Planarity : 0.004 0.055 2508 Dihedral : 3.749 21.228 2000 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.61 % Allowed : 22.07 % Favored : 75.32 % 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: -0.80 (0.20), residues: 1824 helix: 1.71 (0.21), residues: 654 sheet: -1.07 (0.26), residues: 368 loop : -2.26 (0.20), residues: 802 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 376 time to evaluate : 1.525 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 388 average time/residue: 0.2892 time to fit residues: 163.0429 Evaluate side-chains 372 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 347 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1332 time to fit residues: 8.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 0.0000 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 0.0980 chunk 0 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 158 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 158 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14698 Z= 0.180 Angle : 0.525 8.338 19916 Z= 0.268 Chirality : 0.039 0.134 2248 Planarity : 0.003 0.053 2508 Dihedral : 3.646 22.366 2000 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.91 % Allowed : 22.71 % Favored : 75.38 % 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: -0.63 (0.20), residues: 1824 helix: 1.97 (0.21), residues: 638 sheet: -0.89 (0.26), residues: 378 loop : -2.26 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 375 time to evaluate : 1.640 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 392 average time/residue: 0.2717 time to fit residues: 153.9803 Evaluate side-chains 368 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 359 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1391 time to fit residues: 4.6212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 0.0010 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 351 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14698 Z= 0.464 Angle : 0.681 11.544 19916 Z= 0.350 Chirality : 0.045 0.193 2248 Planarity : 0.004 0.053 2508 Dihedral : 4.213 24.123 2000 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.69 % Allowed : 23.22 % Favored : 73.09 % 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: -0.95 (0.20), residues: 1824 helix: 1.51 (0.21), residues: 654 sheet: -0.80 (0.26), residues: 370 loop : -2.47 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 354 time to evaluate : 1.807 Fit side-chains outliers start: 58 outliers final: 37 residues processed: 376 average time/residue: 0.2717 time to fit residues: 147.6328 Evaluate side-chains 381 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 344 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1364 time to fit residues: 11.7791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 98 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 0.0060 chunk 108 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.0270 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 158 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 158 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14698 Z= 0.166 Angle : 0.554 9.209 19916 Z= 0.281 Chirality : 0.039 0.136 2248 Planarity : 0.003 0.052 2508 Dihedral : 3.805 23.859 2000 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.59 % Allowed : 24.43 % Favored : 73.98 % 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: -0.61 (0.20), residues: 1824 helix: 1.76 (0.21), residues: 652 sheet: -0.79 (0.26), residues: 368 loop : -2.13 (0.21), residues: 804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 394 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 403 average time/residue: 0.2784 time to fit residues: 161.9131 Evaluate side-chains 394 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 380 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1417 time to fit residues: 5.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14698 Z= 0.240 Angle : 0.583 10.228 19916 Z= 0.295 Chirality : 0.041 0.156 2248 Planarity : 0.004 0.053 2508 Dihedral : 3.811 23.248 2000 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.53 % Allowed : 25.57 % Favored : 72.90 % 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: -0.57 (0.20), residues: 1824 helix: 1.78 (0.21), residues: 654 sheet: -0.61 (0.26), residues: 372 loop : -2.20 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 367 time to evaluate : 1.690 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 374 average time/residue: 0.2931 time to fit residues: 156.8437 Evaluate side-chains 374 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 358 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1658 time to fit residues: 6.8471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 146 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 158 ASN A 351 GLN B 141 GLN B 158 ASN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14698 Z= 0.173 Angle : 0.553 11.140 19916 Z= 0.279 Chirality : 0.039 0.172 2248 Planarity : 0.003 0.051 2508 Dihedral : 3.694 22.408 2000 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.83 % Allowed : 25.89 % Favored : 73.28 % 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: -0.36 (0.20), residues: 1824 helix: 2.04 (0.21), residues: 636 sheet: -0.52 (0.26), residues: 372 loop : -2.06 (0.21), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 389 time to evaluate : 1.596 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 392 average time/residue: 0.2852 time to fit residues: 160.0867 Evaluate side-chains 384 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 379 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1384 time to fit residues: 3.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14698 Z= 0.281 Angle : 0.603 12.645 19916 Z= 0.308 Chirality : 0.042 0.175 2248 Planarity : 0.004 0.052 2508 Dihedral : 3.834 22.471 2000 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.51 % Allowed : 26.46 % Favored : 73.03 % 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: -0.50 (0.20), residues: 1824 helix: 1.81 (0.21), residues: 654 sheet: -0.63 (0.26), residues: 378 loop : -2.11 (0.21), residues: 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 373 time to evaluate : 1.740 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 374 average time/residue: 0.2809 time to fit residues: 151.4246 Evaluate side-chains 376 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 371 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1462 time to fit residues: 3.6100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 125 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 158 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 158 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106598 restraints weight = 19893.073| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.70 r_work: 0.3155 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14698 Z= 0.209 Angle : 0.578 12.090 19916 Z= 0.294 Chirality : 0.040 0.176 2248 Planarity : 0.003 0.051 2508 Dihedral : 3.776 22.388 2000 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.76 % Allowed : 26.27 % Favored : 72.96 % 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: -0.39 (0.20), residues: 1824 helix: 2.02 (0.21), residues: 636 sheet: -0.59 (0.26), residues: 378 loop : -2.05 (0.20), residues: 810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.08 seconds wall clock time: 72 minutes 57.95 seconds (4377.95 seconds total)