Starting phenix.real_space_refine on Sat Feb 17 17:25:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6r_25725/02_2024/7t6r_25725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6r_25725/02_2024/7t6r_25725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6r_25725/02_2024/7t6r_25725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6r_25725/02_2024/7t6r_25725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6r_25725/02_2024/7t6r_25725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6r_25725/02_2024/7t6r_25725.pdb" } resolution = 3.0 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= 0.007 sd= 0.033 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 10.49, per 1000 atoms: 0.54 Number of scatterers: 19412 At special positions: 0 Unit cell: (138.61, 138.61, 121.18, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.50 Conformation dependent library (CDL) restraints added in 3.7 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 8 sheets defined 65.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.557A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.940A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.239A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.735A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.914A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.525A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.771A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.806A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.139A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.538A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.503A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.581A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 510 removed outlier: 4.180A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.609A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.584A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.848A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.806A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.608A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.973A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.284A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.725A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.959A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.660A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.777A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.818A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.523A pdb=" N TYR B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.500A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.518A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 446 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.615A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 510 removed outlier: 4.165A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.651A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.593A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 4.113A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 604 removed outlier: 3.818A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.948A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.288A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.759A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.848A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.705A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.860A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 3.544A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.808A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.140A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.530A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.519A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 446 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.624A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 510 removed outlier: 4.187A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.586A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.590A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 585 removed outlier: 4.048A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 604 removed outlier: 3.804A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.591A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.917A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.275A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.738A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.841A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.527A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.785A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.504A pdb=" N LEU D 234 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 262 removed outlier: 4.008A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.503A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.127A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.531A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.517A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 446 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.579A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 510 removed outlier: 4.170A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.687A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.577A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 585 removed outlier: 4.045A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 604 removed outlier: 3.821A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.835A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.842A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.842A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.844A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1086 hydrogen bonds defined for protein. 3177 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: 5.92 Time building geometry restraints manager: 7.99 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: 4991 1.34 - 1.45: 3870 1.45 - 1.57: 10771 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C GLU D 113 " pdb=" N PRO D 114 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.59e+01 bond pdb=" C GLU A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.54e+01 bond pdb=" C GLU B 113 " pdb=" N PRO B 114 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.53e+01 bond pdb=" C GLU C 113 " pdb=" N PRO C 114 " ideal model delta sigma weight residual 1.337 1.385 -0.048 1.24e-02 6.50e+03 1.52e+01 bond pdb=" N ASP C 627 " pdb=" CA ASP C 627 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.72e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 97.64 - 104.96: 377 104.96 - 112.28: 9434 112.28 - 119.60: 7480 119.60 - 126.91: 9377 126.91 - 134.23: 296 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C LEU D 604 " pdb=" N GLU D 605 " pdb=" CA GLU D 605 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C LEU A 604 " pdb=" N GLU A 605 " pdb=" CA GLU A 605 " ideal model delta sigma weight residual 121.54 133.32 -11.78 1.91e+00 2.74e-01 3.81e+01 angle pdb=" C LEU C 604 " pdb=" N GLU C 605 " pdb=" CA GLU C 605 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C LEU B 604 " pdb=" N GLU B 605 " pdb=" CA GLU B 605 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C GLY D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 10534 16.65 - 33.31: 1013 33.31 - 49.96: 202 49.96 - 66.61: 39 66.61 - 83.26: 24 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE C 510 " pdb=" C ILE C 510 " pdb=" N THR C 511 " pdb=" CA THR C 511 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA ILE D 510 " pdb=" C ILE D 510 " pdb=" N THR D 511 " pdb=" CA THR D 511 " ideal model delta harmonic sigma weight residual 180.00 147.19 32.81 0 5.00e+00 4.00e-02 4.31e+01 dihedral pdb=" CA ILE A 510 " pdb=" C ILE A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 147.25 32.75 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2585 0.074 - 0.148: 395 0.148 - 0.222: 77 0.222 - 0.296: 11 0.296 - 0.369: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 511 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C THR D 511 " 0.050 2.00e-02 2.50e+03 pdb=" O THR D 511 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE D 512 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 511 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C THR B 511 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 511 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE B 512 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 511 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C THR A 511 " -0.050 2.00e-02 2.50e+03 pdb=" O THR A 511 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 512 " 0.017 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6243 2.85 - 3.36: 18010 3.36 - 3.87: 32961 3.87 - 4.39: 38676 4.39 - 4.90: 65671 Nonbonded interactions: 161561 Sorted by model distance: nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.335 2.440 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.337 2.440 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.344 2.440 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.345 2.440 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 415 " model vdw 2.359 2.440 ... (remaining 161556 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.770 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: 6.170 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 51.520 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.005 0.063 19860 Z= 0.331 Angle : 1.072 12.183 26964 Z= 0.567 Chirality : 0.058 0.369 3072 Planarity : 0.008 0.063 3416 Dihedral : 14.253 83.263 7236 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.13), residues: 2408 helix: -2.09 (0.10), residues: 1484 sheet: -2.20 (0.52), residues: 64 loop : -1.96 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 583 HIS 0.010 0.001 HIS D 157 PHE 0.039 0.002 PHE C 456 TYR 0.025 0.002 TYR C 621 ARG 0.013 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.040 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 1.2764 time to fit residues: 391.9302 Evaluate side-chains 193 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 0.2980 chunk 72 optimal weight: 0.0870 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 185 HIS B 128 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 185 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19860 Z= 0.147 Angle : 0.556 7.818 26964 Z= 0.289 Chirality : 0.039 0.132 3072 Planarity : 0.005 0.046 3416 Dihedral : 4.800 24.960 2644 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.86 % Allowed : 9.59 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 2408 helix: -0.12 (0.12), residues: 1504 sheet: -1.12 (0.57), residues: 56 loop : -1.64 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 583 HIS 0.002 0.001 HIS A 258 PHE 0.012 0.001 PHE D 537 TYR 0.011 0.001 TYR A 161 ARG 0.003 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 2.206 Fit side-chains REVERT: A 215 MET cc_start: 0.8931 (tpt) cc_final: 0.8679 (tpt) REVERT: B 290 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5517 (pt) REVERT: B 554 MET cc_start: 0.7839 (tpt) cc_final: 0.7633 (tpt) REVERT: C 290 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5536 (pt) outliers start: 18 outliers final: 4 residues processed: 231 average time/residue: 1.3102 time to fit residues: 340.9725 Evaluate side-chains 183 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 189 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 214 GLN A 261 GLN A 369 GLN A 446 ASN B 185 HIS B 192 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 369 GLN B 446 ASN C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 369 GLN C 446 ASN D 185 HIS D 192 GLN D 214 GLN D 369 GLN D 446 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19860 Z= 0.213 Angle : 0.568 8.427 26964 Z= 0.294 Chirality : 0.040 0.151 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.563 23.721 2644 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.67 % Allowed : 13.17 % Favored : 85.16 % 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: -0.17 (0.17), residues: 2408 helix: 0.75 (0.13), residues: 1512 sheet: -2.31 (0.42), residues: 116 loop : -1.37 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 593 HIS 0.004 0.001 HIS B 201 PHE 0.015 0.001 PHE A 537 TYR 0.013 0.001 TYR C 216 ARG 0.008 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 2.475 Fit side-chains REVERT: A 146 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7574 (mmm-85) REVERT: A 491 MET cc_start: 0.6767 (mtp) cc_final: 0.6546 (mtt) REVERT: B 146 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7561 (mmm-85) REVERT: B 290 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.5690 (pt) REVERT: C 195 LEU cc_start: 0.7868 (mp) cc_final: 0.7632 (mt) REVERT: C 290 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.5715 (pt) REVERT: D 146 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7573 (mmm-85) outliers start: 35 outliers final: 11 residues processed: 218 average time/residue: 1.2635 time to fit residues: 312.8941 Evaluate side-chains 195 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 0.0970 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 51 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19860 Z= 0.145 Angle : 0.522 11.009 26964 Z= 0.268 Chirality : 0.038 0.133 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.362 24.076 2644 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.05 % Allowed : 15.55 % Favored : 83.40 % 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: 0.22 (0.17), residues: 2408 helix: 1.13 (0.13), residues: 1504 sheet: -2.22 (0.43), residues: 116 loop : -1.37 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 593 HIS 0.002 0.000 HIS B 201 PHE 0.011 0.001 PHE D 537 TYR 0.012 0.001 TYR A 555 ARG 0.006 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 2.394 Fit side-chains REVERT: A 491 MET cc_start: 0.6772 (mtp) cc_final: 0.6543 (mtt) REVERT: B 290 LEU cc_start: 0.6466 (tp) cc_final: 0.5623 (pt) REVERT: B 612 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 290 LEU cc_start: 0.6500 (tp) cc_final: 0.5671 (pt) REVERT: C 554 MET cc_start: 0.8223 (tpt) cc_final: 0.7711 (tpt) REVERT: D 146 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7704 (mmm-85) REVERT: D 554 MET cc_start: 0.8136 (tpt) cc_final: 0.7679 (tpt) outliers start: 22 outliers final: 4 residues processed: 207 average time/residue: 1.2277 time to fit residues: 289.5213 Evaluate side-chains 193 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19860 Z= 0.146 Angle : 0.519 12.314 26964 Z= 0.265 Chirality : 0.038 0.134 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.231 23.256 2644 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.77 % Allowed : 15.08 % Favored : 83.16 % 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: 0.47 (0.17), residues: 2408 helix: 1.32 (0.13), residues: 1508 sheet: -2.19 (0.43), residues: 116 loop : -1.25 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 593 HIS 0.002 0.000 HIS D 201 PHE 0.011 0.001 PHE D 537 TYR 0.011 0.001 TYR A 555 ARG 0.008 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 2.347 Fit side-chains REVERT: A 46 ASP cc_start: 0.7618 (m-30) cc_final: 0.7386 (m-30) REVERT: A 146 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7577 (mmm-85) REVERT: A 491 MET cc_start: 0.6827 (mtp) cc_final: 0.6595 (mtt) REVERT: A 528 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8709 (m) REVERT: B 146 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7565 (mmm-85) REVERT: B 290 LEU cc_start: 0.6475 (tp) cc_final: 0.5586 (pt) REVERT: B 528 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8711 (m) REVERT: B 554 MET cc_start: 0.8075 (tpt) cc_final: 0.7683 (tpt) REVERT: C 290 LEU cc_start: 0.6482 (tp) cc_final: 0.5601 (pt) REVERT: C 528 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8712 (m) REVERT: D 131 ASN cc_start: 0.8404 (m-40) cc_final: 0.8074 (m-40) REVERT: D 146 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7731 (mmm-85) REVERT: D 528 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8703 (m) REVERT: D 554 MET cc_start: 0.8131 (tpt) cc_final: 0.7735 (tpt) outliers start: 37 outliers final: 15 residues processed: 220 average time/residue: 1.2142 time to fit residues: 304.5340 Evaluate side-chains 206 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.0270 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.0370 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 51 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 369 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19860 Z= 0.125 Angle : 0.494 9.660 26964 Z= 0.253 Chirality : 0.037 0.124 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.088 23.341 2644 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.81 % Allowed : 15.51 % Favored : 82.68 % 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: 0.69 (0.17), residues: 2408 helix: 1.51 (0.13), residues: 1508 sheet: -2.23 (0.43), residues: 116 loop : -1.17 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 583 HIS 0.002 0.000 HIS C 185 PHE 0.010 0.001 PHE C 611 TYR 0.009 0.001 TYR A 555 ARG 0.007 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 2.280 Fit side-chains REVERT: A 131 ASN cc_start: 0.8216 (m-40) cc_final: 0.8014 (m-40) REVERT: A 146 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7609 (mmm-85) REVERT: A 491 MET cc_start: 0.6807 (mtp) cc_final: 0.6568 (mtt) REVERT: A 554 MET cc_start: 0.8121 (tpt) cc_final: 0.7681 (tpt) REVERT: B 46 ASP cc_start: 0.7513 (m-30) cc_final: 0.7310 (m-30) REVERT: B 146 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7583 (mmm-85) REVERT: B 290 LEU cc_start: 0.6416 (tp) cc_final: 0.5493 (pt) REVERT: B 554 MET cc_start: 0.8017 (tpt) cc_final: 0.7732 (tpt) REVERT: C 290 LEU cc_start: 0.6394 (tp) cc_final: 0.5483 (pt) REVERT: C 554 MET cc_start: 0.8092 (tpt) cc_final: 0.7658 (tpt) REVERT: D 131 ASN cc_start: 0.8378 (m-40) cc_final: 0.8075 (m-40) REVERT: D 146 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7699 (mmm-85) REVERT: D 554 MET cc_start: 0.8082 (tpt) cc_final: 0.7709 (tpt) outliers start: 38 outliers final: 9 residues processed: 245 average time/residue: 1.2658 time to fit residues: 350.7727 Evaluate side-chains 204 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 214 GLN D 369 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.175 Angle : 0.538 11.173 26964 Z= 0.274 Chirality : 0.039 0.141 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.154 22.783 2644 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.91 % Allowed : 16.36 % Favored : 81.73 % 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: 0.69 (0.17), residues: 2408 helix: 1.52 (0.13), residues: 1508 sheet: -2.20 (0.43), residues: 116 loop : -1.20 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 583 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE A 537 TYR 0.010 0.001 TYR A 555 ARG 0.005 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.521 Fit side-chains revert: symmetry clash REVERT: A 131 ASN cc_start: 0.8226 (m-40) cc_final: 0.8014 (m-40) REVERT: A 146 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7727 (mmm-85) REVERT: A 491 MET cc_start: 0.6857 (mtp) cc_final: 0.6630 (mtt) REVERT: B 46 ASP cc_start: 0.7492 (m-30) cc_final: 0.7274 (m-30) REVERT: B 146 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7705 (mmm-85) REVERT: B 195 LEU cc_start: 0.7642 (mp) cc_final: 0.7332 (mt) REVERT: B 554 MET cc_start: 0.8117 (tpt) cc_final: 0.7760 (tpt) REVERT: C 290 LEU cc_start: 0.6523 (tp) cc_final: 0.5621 (pt) REVERT: C 554 MET cc_start: 0.8172 (tpt) cc_final: 0.7742 (tpt) REVERT: D 131 ASN cc_start: 0.8322 (m-40) cc_final: 0.8026 (m-40) REVERT: D 146 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7774 (mmm-85) REVERT: D 554 MET cc_start: 0.8188 (tpt) cc_final: 0.7834 (tpt) REVERT: D 612 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8800 (mt) outliers start: 40 outliers final: 19 residues processed: 224 average time/residue: 1.1894 time to fit residues: 303.8809 Evaluate side-chains 211 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 0.0370 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 181 optimal weight: 3.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.130 Angle : 0.509 9.626 26964 Z= 0.260 Chirality : 0.038 0.149 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.070 23.740 2644 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.72 % Allowed : 16.27 % Favored : 82.01 % 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: 0.86 (0.17), residues: 2408 helix: 1.65 (0.13), residues: 1508 sheet: -2.18 (0.44), residues: 116 loop : -1.09 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 583 HIS 0.002 0.000 HIS A 201 PHE 0.010 0.001 PHE D 611 TYR 0.009 0.001 TYR A 555 ARG 0.006 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 2.247 Fit side-chains REVERT: A 146 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7716 (mmm-85) REVERT: A 491 MET cc_start: 0.6818 (mtp) cc_final: 0.6597 (mtt) REVERT: A 554 MET cc_start: 0.8100 (tpt) cc_final: 0.7614 (tpt) REVERT: B 146 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7674 (mmm-85) REVERT: B 554 MET cc_start: 0.8038 (tpt) cc_final: 0.7718 (tpt) REVERT: C 554 MET cc_start: 0.8152 (tpt) cc_final: 0.7658 (tpt) REVERT: D 131 ASN cc_start: 0.8245 (m-40) cc_final: 0.7979 (m-40) REVERT: D 146 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7757 (mmm-85) REVERT: D 554 MET cc_start: 0.8096 (tpt) cc_final: 0.7755 (tpt) outliers start: 36 outliers final: 18 residues processed: 227 average time/residue: 1.2563 time to fit residues: 325.4654 Evaluate side-chains 205 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 194 optimal weight: 0.3980 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19860 Z= 0.152 Angle : 0.525 9.217 26964 Z= 0.268 Chirality : 0.038 0.137 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.083 23.041 2644 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.29 % Allowed : 17.22 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2408 helix: 1.67 (0.13), residues: 1508 sheet: -2.17 (0.44), residues: 116 loop : -1.08 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 583 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.001 PHE C 537 TYR 0.012 0.001 TYR A 555 ARG 0.005 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7737 (mmm-85) REVERT: A 491 MET cc_start: 0.6846 (mtp) cc_final: 0.6627 (mtt) REVERT: A 554 MET cc_start: 0.8104 (tpt) cc_final: 0.7643 (tpt) REVERT: B 146 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7703 (mmm-85) REVERT: B 554 MET cc_start: 0.8070 (tpt) cc_final: 0.7733 (tpt) REVERT: C 554 MET cc_start: 0.8189 (tpt) cc_final: 0.7756 (tpt) REVERT: D 131 ASN cc_start: 0.8220 (m-40) cc_final: 0.7991 (m-40) REVERT: D 146 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7779 (mmm-85) REVERT: D 554 MET cc_start: 0.8112 (tpt) cc_final: 0.7834 (tpt) outliers start: 27 outliers final: 20 residues processed: 211 average time/residue: 1.2745 time to fit residues: 304.6271 Evaluate side-chains 205 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 158 optimal weight: 0.0170 chunk 239 optimal weight: 0.3980 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19860 Z= 0.145 Angle : 0.523 9.995 26964 Z= 0.267 Chirality : 0.038 0.137 3072 Planarity : 0.004 0.043 3416 Dihedral : 4.069 23.282 2644 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.95 % Allowed : 17.37 % Favored : 81.68 % 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: 0.91 (0.17), residues: 2408 helix: 1.67 (0.13), residues: 1508 sheet: -2.17 (0.44), residues: 116 loop : -1.05 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 583 HIS 0.002 0.000 HIS B 201 PHE 0.010 0.001 PHE A 537 TYR 0.010 0.001 TYR A 555 ARG 0.005 0.000 ARG B 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.391 Fit side-chains REVERT: A 146 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7736 (mmm-85) REVERT: A 491 MET cc_start: 0.6857 (mtp) cc_final: 0.6632 (mtt) REVERT: A 554 MET cc_start: 0.8103 (tpt) cc_final: 0.7639 (tpt) REVERT: B 146 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7712 (mmm-85) REVERT: B 554 MET cc_start: 0.8070 (tpt) cc_final: 0.7714 (tpt) REVERT: C 554 MET cc_start: 0.8207 (tpt) cc_final: 0.7788 (tpt) REVERT: D 146 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7779 (mmm-85) REVERT: D 554 MET cc_start: 0.8134 (tpt) cc_final: 0.7821 (tpt) outliers start: 20 outliers final: 18 residues processed: 198 average time/residue: 1.3654 time to fit residues: 304.5933 Evaluate side-chains 200 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127325 restraints weight = 23008.495| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.70 r_work: 0.3335 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.154 Angle : 0.536 10.354 26964 Z= 0.274 Chirality : 0.038 0.166 3072 Planarity : 0.004 0.043 3416 Dihedral : 4.099 23.210 2644 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.95 % Allowed : 17.89 % Favored : 81.15 % 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: 0.93 (0.17), residues: 2408 helix: 1.68 (0.13), residues: 1504 sheet: -2.15 (0.44), residues: 116 loop : -1.00 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 583 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.001 PHE A 537 TYR 0.010 0.001 TYR A 555 ARG 0.005 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.15 seconds wall clock time: 110 minutes 24.39 seconds (6624.39 seconds total)