Starting phenix.real_space_refine on Sun Jul 21 12:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/07_2024/8p7w_17537.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/07_2024/8p7w_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_17537/07_2024/8p7w_17537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/07_2024/8p7w_17537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/07_2024/8p7w_17537.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7w_17537/07_2024/8p7w_17537.cif" } 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-dev-5388/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: 8.55, per 1000 atoms: 0.59 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: 5.54 Conformation dependent library (CDL) restraints added in 3.0 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: 1.64 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: 4.60 Time building geometry restraints manager: 5.87 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: 2.330 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: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.880 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 36 HIS 0.009 0.001 HIS A 155 PHE 0.032 0.001 PHE C 68 TYR 0.012 0.001 TYR B 463 ARG 0.006 0.001 ARG Y 101 *********************** 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 : 1.680 Fit side-chains REVERT: B 393 GLN cc_start: 0.7833 (pp30) cc_final: 0.7587 (mt0) REVERT: B 481 MET cc_start: 0.8443 (tpp) cc_final: 0.8227 (mmm) REVERT: D 77 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7804 (t0) REVERT: D 78 GLN cc_start: 0.8200 (mt0) cc_final: 0.7522 (mp10) REVERT: F 13 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7203 (ptmm) REVERT: F 70 ILE cc_start: 0.8305 (mm) cc_final: 0.8076 (mt) REVERT: F 77 ASN cc_start: 0.8889 (t0) cc_final: 0.8663 (t0) REVERT: F 78 GLN cc_start: 0.7901 (pt0) cc_final: 0.7451 (pt0) REVERT: F 111 GLN cc_start: 0.7305 (mp10) cc_final: 0.7081 (mp10) REVERT: G 17 ASP cc_start: 0.7813 (m-30) cc_final: 0.7431 (m-30) outliers start: 7 outliers final: 1 residues processed: 385 average time/residue: 0.2698 time to fit residues: 149.2634 Evaluate side-chains 360 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain D residue 77 ASN 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 ** 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: 0.8481 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14698 Z= 0.184 Angle : 0.526 7.689 19916 Z= 0.269 Chirality : 0.039 0.136 2248 Planarity : 0.003 0.069 2508 Dihedral : 3.777 33.595 2004 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.88 % Allowed : 19.97 % Favored : 76.15 % 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: -1.07 (0.20), residues: 1824 helix: 1.48 (0.21), residues: 652 sheet: -1.18 (0.26), residues: 392 loop : -2.45 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 36 HIS 0.007 0.001 HIS A 155 PHE 0.020 0.001 PHE C 68 TYR 0.015 0.001 TYR B 463 ARG 0.006 0.000 ARG B 147 *********************** 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 453 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 392 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 43 CYS cc_start: 0.6902 (m) cc_final: 0.6379 (m) REVERT: A 398 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: A 417 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8361 (mmmm) REVERT: A 541 MET cc_start: 0.8306 (mtm) cc_final: 0.7964 (ttm) REVERT: C 36 TRP cc_start: 0.8823 (m100) cc_final: 0.8618 (m100) REVERT: D 78 GLN cc_start: 0.8182 (mt0) cc_final: 0.7500 (mp10) REVERT: E 39 LYS cc_start: 0.8238 (mmtp) cc_final: 0.8015 (mmtp) REVERT: F 13 LYS cc_start: 0.7549 (mtpp) cc_final: 0.7080 (ptmm) REVERT: F 70 ILE cc_start: 0.8460 (mm) cc_final: 0.8200 (mt) REVERT: F 78 GLN cc_start: 0.7995 (pt0) cc_final: 0.7608 (pm20) REVERT: G 17 ASP cc_start: 0.7866 (m-30) cc_final: 0.7444 (m-30) outliers start: 61 outliers final: 33 residues processed: 418 average time/residue: 0.2714 time to fit residues: 165.2833 Evaluate side-chains 395 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 361 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 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 77 ASN Y 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14698 Z= 0.224 Angle : 0.534 7.672 19916 Z= 0.273 Chirality : 0.040 0.149 2248 Planarity : 0.003 0.060 2508 Dihedral : 3.689 20.553 2000 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.71 % Allowed : 20.55 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1824 helix: 1.63 (0.21), residues: 654 sheet: -1.07 (0.26), residues: 378 loop : -2.39 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 36 HIS 0.004 0.001 HIS A 155 PHE 0.017 0.001 PHE B 293 TYR 0.013 0.001 TYR B 463 ARG 0.005 0.000 ARG B 191 *********************** 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 439 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 365 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: A 402 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8492 (t) REVERT: A 417 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8328 (mmmm) REVERT: D 72 ARG cc_start: 0.8673 (ptt180) cc_final: 0.8462 (ptt180) REVERT: E 11 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: E 39 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7973 (mmtp) REVERT: F 13 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7238 (ptmm) REVERT: F 70 ILE cc_start: 0.8434 (mm) cc_final: 0.8189 (mm) REVERT: F 78 GLN cc_start: 0.8069 (pt0) cc_final: 0.7645 (pm20) REVERT: G 17 ASP cc_start: 0.7904 (m-30) cc_final: 0.7476 (m-30) REVERT: Y 73 ASP cc_start: 0.8629 (t0) cc_final: 0.8404 (t0) outliers start: 74 outliers final: 46 residues processed: 395 average time/residue: 0.2667 time to fit residues: 153.1419 Evaluate side-chains 411 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 362 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Y 74 ASN Y 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14698 Z= 0.267 Angle : 0.557 8.296 19916 Z= 0.285 Chirality : 0.041 0.157 2248 Planarity : 0.004 0.057 2508 Dihedral : 3.821 20.449 2000 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.60 % Allowed : 20.04 % Favored : 74.36 % 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: -0.81 (0.20), residues: 1824 helix: 1.70 (0.21), residues: 654 sheet: -0.96 (0.26), residues: 378 loop : -2.34 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 36 HIS 0.004 0.001 HIS A 583 PHE 0.017 0.001 PHE A 293 TYR 0.015 0.001 TYR B 463 ARG 0.004 0.001 ARG B 147 *********************** 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 455 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 367 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8511 (t) REVERT: B 398 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: D 81 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7807 (tp) REVERT: D 107 ASP cc_start: 0.8777 (m-30) cc_final: 0.8506 (m-30) REVERT: E 11 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: F 70 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (mm) REVERT: F 78 GLN cc_start: 0.8191 (pt0) cc_final: 0.7763 (pm20) REVERT: G 17 ASP cc_start: 0.8034 (m-30) cc_final: 0.7584 (m-30) REVERT: Y 73 ASP cc_start: 0.8637 (t0) cc_final: 0.8377 (t0) outliers start: 88 outliers final: 61 residues processed: 405 average time/residue: 0.2622 time to fit residues: 153.8113 Evaluate side-chains 416 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 350 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 148 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 88 optimal weight: 0.0270 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 158 ASN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14698 Z= 0.177 Angle : 0.525 7.884 19916 Z= 0.265 Chirality : 0.039 0.135 2248 Planarity : 0.003 0.053 2508 Dihedral : 3.642 21.422 2000 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.83 % Allowed : 22.01 % Favored : 73.16 % 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: -0.54 (0.20), residues: 1824 helix: 2.07 (0.21), residues: 636 sheet: -0.89 (0.26), residues: 388 loop : -2.19 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 35 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE A 293 TYR 0.018 0.001 TYR B 463 ARG 0.005 0.000 ARG B 147 *********************** 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 471 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 395 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8039 (t0) REVERT: A 398 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: A 502 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8784 (mmtm) REVERT: B 43 CYS cc_start: 0.6667 (m) cc_final: 0.6327 (m) REVERT: B 398 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: B 454 LEU cc_start: 0.8938 (tp) cc_final: 0.8276 (tp) REVERT: D 81 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7822 (tp) REVERT: D 107 ASP cc_start: 0.8797 (m-30) cc_final: 0.8520 (m-30) REVERT: E 11 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: F 13 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7156 (ptmm) REVERT: F 78 GLN cc_start: 0.8009 (pt0) cc_final: 0.7589 (pm20) REVERT: G 17 ASP cc_start: 0.8057 (m-30) cc_final: 0.7663 (m-30) REVERT: Y 73 ASP cc_start: 0.8640 (t0) cc_final: 0.8374 (t0) outliers start: 76 outliers final: 48 residues processed: 428 average time/residue: 0.2585 time to fit residues: 160.6991 Evaluate side-chains 422 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 369 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP 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: 2.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.0020 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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** B 141 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Y 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 14698 Z= 0.498 Angle : 0.690 11.539 19916 Z= 0.357 Chirality : 0.046 0.202 2248 Planarity : 0.004 0.054 2508 Dihedral : 4.263 22.494 2000 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 6.30 % Allowed : 21.63 % Favored : 72.07 % 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: 1.47 (0.21), residues: 654 sheet: -0.87 (0.26), residues: 376 loop : -2.41 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 37 HIS 0.006 0.002 HIS A 583 PHE 0.021 0.002 PHE A 293 TYR 0.029 0.002 TYR B 463 ARG 0.007 0.001 ARG B 191 *********************** 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 453 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 354 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8944 (mp) REVERT: A 398 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7185 (mp-120) REVERT: A 402 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8549 (t) REVERT: B 98 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8519 (p0) REVERT: B 398 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: B 458 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: D 65 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6871 (ptp90) REVERT: D 81 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8060 (tp) REVERT: D 107 ASP cc_start: 0.8769 (m-30) cc_final: 0.8531 (m-30) REVERT: E 11 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: E 24 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6558 (mtmm) REVERT: F 78 GLN cc_start: 0.8250 (pt0) cc_final: 0.7576 (pm20) REVERT: F 82 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7416 (tm-30) REVERT: G 17 ASP cc_start: 0.8055 (m-30) cc_final: 0.7617 (m-30) outliers start: 99 outliers final: 67 residues processed: 402 average time/residue: 0.2652 time to fit residues: 155.0448 Evaluate side-chains 423 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 346 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.8532 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14698 Z= 0.196 Angle : 0.578 11.823 19916 Z= 0.290 Chirality : 0.040 0.135 2248 Planarity : 0.003 0.052 2508 Dihedral : 3.900 21.945 2000 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.77 % Allowed : 24.17 % Favored : 71.06 % 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: -0.73 (0.20), residues: 1824 helix: 1.72 (0.21), residues: 652 sheet: -0.96 (0.25), residues: 378 loop : -2.21 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35 HIS 0.004 0.001 HIS A 155 PHE 0.016 0.001 PHE B 293 TYR 0.024 0.001 TYR B 463 ARG 0.005 0.000 ARG B 191 *********************** 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 458 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 383 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8600 (m110) cc_final: 0.8065 (t0) REVERT: A 148 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8885 (mp) REVERT: A 336 TYR cc_start: 0.9201 (t80) cc_final: 0.8903 (t80) REVERT: A 398 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: A 458 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8067 (mp0) REVERT: B 398 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: B 458 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: D 107 ASP cc_start: 0.8773 (m-30) cc_final: 0.8519 (m-30) REVERT: E 11 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: F 13 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7311 (ptmm) REVERT: F 78 GLN cc_start: 0.8124 (pt0) cc_final: 0.7717 (pm20) REVERT: F 82 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7471 (tm-30) REVERT: G 17 ASP cc_start: 0.8145 (m-30) cc_final: 0.7745 (m-30) outliers start: 75 outliers final: 46 residues processed: 416 average time/residue: 0.2635 time to fit residues: 158.6084 Evaluate side-chains 431 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 380 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP 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: 0.6980 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 136 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14698 Z= 0.196 Angle : 0.556 9.116 19916 Z= 0.281 Chirality : 0.040 0.157 2248 Planarity : 0.003 0.052 2508 Dihedral : 3.731 21.394 2000 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.13 % Allowed : 24.43 % Favored : 71.44 % 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: -0.44 (0.20), residues: 1824 helix: 2.05 (0.21), residues: 636 sheet: -0.72 (0.25), residues: 392 loop : -2.10 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE B 293 TYR 0.018 0.001 TYR B 463 ARG 0.004 0.000 ARG B 191 *********************** 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 456 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 391 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8607 (m110) cc_final: 0.8064 (t0) REVERT: A 458 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7982 (mp0) REVERT: A 502 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8777 (mmtm) REVERT: B 43 CYS cc_start: 0.6894 (m) cc_final: 0.6429 (m) REVERT: B 398 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: B 458 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: D 78 GLN cc_start: 0.8126 (mt0) cc_final: 0.7362 (pm20) REVERT: E 11 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: F 13 LYS cc_start: 0.7839 (mtpp) cc_final: 0.7241 (ptmm) REVERT: F 78 GLN cc_start: 0.8196 (pt0) cc_final: 0.7813 (pm20) REVERT: F 82 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7462 (tm-30) REVERT: G 17 ASP cc_start: 0.8140 (m-30) cc_final: 0.7756 (m-30) REVERT: Y 73 ASP cc_start: 0.8491 (t0) cc_final: 0.8289 (t0) outliers start: 65 outliers final: 47 residues processed: 417 average time/residue: 0.2755 time to fit residues: 165.0309 Evaluate side-chains 432 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 382 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.0470 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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** Y 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14698 Z= 0.186 Angle : 0.556 9.246 19916 Z= 0.281 Chirality : 0.040 0.160 2248 Planarity : 0.003 0.052 2508 Dihedral : 3.655 20.737 2000 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.01 % Allowed : 24.49 % Favored : 71.50 % 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: -0.40 (0.20), residues: 1824 helix: 2.07 (0.21), residues: 636 sheet: -0.74 (0.26), residues: 382 loop : -2.03 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE B 293 TYR 0.026 0.001 TYR B 463 ARG 0.006 0.000 ARG B 147 *********************** 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 454 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 391 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8589 (m110) cc_final: 0.8053 (t0) REVERT: A 502 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8755 (mmtm) REVERT: D 78 GLN cc_start: 0.8106 (mt0) cc_final: 0.7315 (pm20) REVERT: E 11 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: F 13 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7234 (ptmm) REVERT: F 78 GLN cc_start: 0.8167 (pt0) cc_final: 0.7800 (pm20) REVERT: F 82 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7480 (tm-30) REVERT: G 17 ASP cc_start: 0.8130 (m-30) cc_final: 0.7768 (m-30) REVERT: Y 73 ASP cc_start: 0.8504 (t0) cc_final: 0.8213 (t0) outliers start: 63 outliers final: 47 residues processed: 417 average time/residue: 0.2899 time to fit residues: 176.3183 Evaluate side-chains 433 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 385 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** B 141 GLN B 351 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14698 Z= 0.415 Angle : 0.674 13.205 19916 Z= 0.346 Chirality : 0.044 0.185 2248 Planarity : 0.004 0.053 2508 Dihedral : 4.047 21.518 2000 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.69 % Allowed : 24.24 % Favored : 72.07 % 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: 1.80 (0.21), residues: 638 sheet: -0.77 (0.25), residues: 400 loop : -2.17 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 37 HIS 0.006 0.002 HIS B 583 PHE 0.019 0.002 PHE A 293 TYR 0.052 0.002 TYR B 463 ARG 0.006 0.001 ARG Y 101 ********************** 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 420 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 362 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 622 SER cc_start: 0.9018 (t) cc_final: 0.8802 (p) REVERT: D 65 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6927 (ptp90) REVERT: D 78 GLN cc_start: 0.8143 (mt0) cc_final: 0.7386 (pm20) REVERT: E 11 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: F 78 GLN cc_start: 0.8274 (pt0) cc_final: 0.7881 (pm20) REVERT: F 82 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7404 (tm-30) REVERT: G 17 ASP cc_start: 0.8151 (m-30) cc_final: 0.7755 (m-30) REVERT: Y 73 ASP cc_start: 0.8616 (t0) cc_final: 0.8355 (t0) outliers start: 58 outliers final: 49 residues processed: 384 average time/residue: 0.2680 time to fit residues: 149.2174 Evaluate side-chains 407 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 356 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** F 77 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 = 0.3693 r_free = 0.3693 target = 0.138696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105601 restraints weight = 19915.731| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.69 r_work: 0.3144 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14698 Z= 0.220 Angle : 0.596 12.238 19916 Z= 0.302 Chirality : 0.041 0.175 2248 Planarity : 0.004 0.052 2508 Dihedral : 3.850 20.987 2000 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.56 % Allowed : 25.00 % Favored : 71.44 % 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: -0.45 (0.20), residues: 1824 helix: 1.96 (0.21), residues: 636 sheet: -0.69 (0.26), residues: 382 loop : -2.05 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 155 PHE 0.017 0.001 PHE A 293 TYR 0.047 0.001 TYR B 463 ARG 0.006 0.000 ARG Y 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.40 seconds wall clock time: 71 minutes 19.33 seconds (4279.33 seconds total)