Starting phenix.real_space_refine on Sat Jul 20 13:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/07_2024/8x52_38059.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/07_2024/8x52_38059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/07_2024/8x52_38059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/07_2024/8x52_38059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/07_2024/8x52_38059.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/07_2024/8x52_38059.cif" } resolution = 2.9 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= -0.001 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 43 5.16 5 C 7142 2.51 5 N 1727 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10907 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 145 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5233 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2424 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.64, per 1000 atoms: 0.61 Number of scatterers: 10907 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 2 15.00 O 1993 8.00 N 1727 7.00 C 7142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS A 242 " distance=1.47 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " 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 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 58.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'E' and resid 30 through 37 removed outlier: 3.614A pdb=" N LEU E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 removed outlier: 3.536A pdb=" N ILE E 41 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 4.052A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.948A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.597A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.888A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.513A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.767A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.072A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.699A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.751A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.775A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.898A pdb=" N VAL B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 Processing helix chain 'B' and resid 158 through 175 removed outlier: 4.032A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.919A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.969A pdb=" N PHE B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.977A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 450 removed outlier: 4.187A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.626A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.903A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.739A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.534A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.768A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.872A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.661A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.790A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.591A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 81 removed outlier: 4.129A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 94 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.550A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.551A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1668 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: 2.97 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 71 1.23 - 1.37: 3543 1.37 - 1.52: 4934 1.52 - 1.67: 2566 1.67 - 1.81: 66 Bond restraints: 11180 Sorted by residual: bond pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 1.467 1.685 -0.218 1.17e-02 7.31e+03 3.48e+02 bond pdb=" C GLY B 384 " pdb=" O GLY B 384 " ideal model delta sigma weight residual 1.236 1.090 0.146 1.08e-02 8.57e+03 1.82e+02 bond pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 1.335 1.501 -0.166 1.38e-02 5.25e+03 1.45e+02 bond pdb=" C PRO B 433 " pdb=" O PRO B 433 " ideal model delta sigma weight residual 1.233 1.080 0.153 1.39e-02 5.18e+03 1.22e+02 bond pdb=" C LEU B 435 " pdb=" O LEU B 435 " ideal model delta sigma weight residual 1.244 1.150 0.094 9.10e-03 1.21e+04 1.07e+02 ... (remaining 11175 not shown) Histogram of bond angle deviations from ideal: 95.00 - 104.81: 206 104.81 - 114.63: 6933 114.63 - 124.44: 7804 124.44 - 134.25: 297 134.25 - 144.07: 3 Bond angle restraints: 15243 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.07 -28.64 1.41e+00 5.03e-01 4.13e+02 angle pdb=" C LEU B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.93 137.02 -17.09 1.07e+00 8.73e-01 2.55e+02 angle pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 120.58 130.94 -10.36 7.40e-01 1.83e+00 1.96e+02 angle pdb=" C LEU B 435 " pdb=" N PRO B 436 " pdb=" CA PRO B 436 " ideal model delta sigma weight residual 119.24 131.85 -12.61 1.04e+00 9.25e-01 1.47e+02 angle pdb=" O LEU B 432 " pdb=" C LEU B 432 " pdb=" N PRO B 433 " ideal model delta sigma weight residual 121.72 111.32 10.40 9.80e-01 1.04e+00 1.13e+02 ... (remaining 15238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 6630 23.49 - 46.98: 207 46.98 - 70.46: 43 70.46 - 93.95: 21 93.95 - 117.44: 18 Dihedral angle restraints: 6919 sinusoidal: 3033 harmonic: 3886 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" C PHE B 386 " pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" CB PHE B 386 " ideal model delta harmonic sigma weight residual -122.60 -104.19 -18.41 0 2.50e+00 1.60e-01 5.42e+01 dihedral pdb=" CB CYS E 28 " pdb=" SG CYS E 28 " pdb=" SG CYS A 242 " pdb=" CB CYS A 242 " ideal model delta sinusoidal sigma weight residual 93.00 30.42 62.58 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1782 0.146 - 0.292: 36 0.292 - 0.438: 10 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA PRO B 433 " pdb=" N PRO B 433 " pdb=" C PRO B 433 " pdb=" CB PRO B 433 " both_signs ideal model delta sigma weight residual False 2.72 3.45 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 1827 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.117 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 573 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 114 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ILE B 114 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 114 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 115 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 284 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C PRO B 284 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO B 284 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 285 " 0.022 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 4391 2.92 - 3.58: 15318 3.58 - 4.24: 25252 4.24 - 4.90: 42436 Nonbonded interactions: 87400 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.598 2.776 nonbonded pdb=" OH TYR B 389 " pdb=" O ALA B 434 " model vdw 2.168 2.440 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.263 2.440 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 2.440 ... (remaining 87395 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.780 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.950 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 : 0.009 0.218 11180 Z= 0.558 Angle : 1.131 28.640 15243 Z= 0.685 Chirality : 0.066 0.730 1830 Planarity : 0.007 0.071 1845 Dihedral : 14.341 117.440 4400 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 0.88 % Allowed : 2.98 % Favored : 96.14 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.18), residues: 1322 helix: -1.90 (0.15), residues: 722 sheet: -1.54 (0.47), residues: 114 loop : -2.97 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.040 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6147 (m110) cc_final: 0.5830 (m110) REVERT: A 37 GLU cc_start: 0.6912 (pt0) cc_final: 0.6573 (pt0) REVERT: A 58 HIS cc_start: 0.6969 (m90) cc_final: 0.6035 (m90) REVERT: A 78 LYS cc_start: 0.6766 (ptpt) cc_final: 0.6278 (pttm) REVERT: A 81 ASP cc_start: 0.5412 (m-30) cc_final: 0.4677 (m-30) REVERT: A 143 ASP cc_start: 0.6268 (t0) cc_final: 0.6011 (t70) REVERT: A 201 LEU cc_start: 0.7606 (mt) cc_final: 0.7318 (mm) REVERT: A 224 VAL cc_start: 0.7972 (m) cc_final: 0.7630 (t) REVERT: A 237 GLN cc_start: 0.6411 (mm-40) cc_final: 0.5699 (tm-30) REVERT: A 357 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7748 (pm20) REVERT: A 374 LEU cc_start: 0.7211 (mt) cc_final: 0.6950 (mp) REVERT: A 391 ARG cc_start: 0.6665 (ttp-110) cc_final: 0.6204 (ttm110) REVERT: A 392 ASN cc_start: 0.7428 (m-40) cc_final: 0.7098 (m-40) REVERT: A 474 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6715 (mp0) REVERT: A 478 ASN cc_start: 0.7820 (m-40) cc_final: 0.7455 (m-40) REVERT: A 500 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7190 (tt0) REVERT: A 509 ASP cc_start: 0.7397 (m-30) cc_final: 0.6425 (p0) REVERT: A 540 GLN cc_start: 0.7852 (tt0) cc_final: 0.7600 (tp40) REVERT: A 543 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6667 (mtm110) REVERT: A 565 TYR cc_start: 0.7732 (m-80) cc_final: 0.7311 (m-80) REVERT: A 666 LYS cc_start: 0.5949 (tptt) cc_final: 0.5542 (ttpt) REVERT: B 80 LYS cc_start: 0.6672 (tptt) cc_final: 0.6377 (tptt) REVERT: B 130 LEU cc_start: 0.7391 (tp) cc_final: 0.7126 (mm) REVERT: B 155 LYS cc_start: 0.7243 (tptt) cc_final: 0.7018 (tttm) REVERT: B 163 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7410 (m-70) REVERT: B 187 LYS cc_start: 0.6847 (mttp) cc_final: 0.6624 (mtmp) REVERT: B 380 LYS cc_start: 0.7257 (mttm) cc_final: 0.6939 (mptt) REVERT: C 52 VAL cc_start: 0.7687 (t) cc_final: 0.7318 (m) REVERT: C 56 LEU cc_start: 0.8019 (mt) cc_final: 0.7763 (mt) REVERT: C 119 TYR cc_start: 0.7007 (t80) cc_final: 0.6754 (t80) REVERT: C 140 ASP cc_start: 0.7438 (m-30) cc_final: 0.7043 (m-30) REVERT: C 146 VAL cc_start: 0.7406 (p) cc_final: 0.7086 (m) REVERT: D 59 ARG cc_start: 0.5719 (ttm170) cc_final: 0.5189 (tmt170) REVERT: D 84 ARG cc_start: 0.6642 (mtt90) cc_final: 0.6361 (mtm180) REVERT: D 91 TYR cc_start: 0.6352 (m-80) cc_final: 0.6149 (m-10) outliers start: 10 outliers final: 7 residues processed: 271 average time/residue: 0.9760 time to fit residues: 289.1252 Evaluate side-chains 168 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 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 163 GLN A 194 GLN A 355 GLN A 358 ASN A 385 GLN A 393 GLN A 454 GLN A 531 ASN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 214 HIS ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS C 58 HIS C 68 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11180 Z= 0.245 Angle : 0.688 9.713 15243 Z= 0.335 Chirality : 0.046 0.332 1830 Planarity : 0.005 0.054 1845 Dihedral : 11.954 106.667 2084 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.51 % Allowed : 11.04 % Favored : 85.45 % 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: -1.26 (0.22), residues: 1322 helix: 0.15 (0.19), residues: 730 sheet: -1.00 (0.49), residues: 107 loop : -2.31 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 209 HIS 0.010 0.002 HIS C 197 PHE 0.040 0.002 PHE A 302 TYR 0.031 0.002 TYR A 645 ARG 0.009 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6753 (tp) REVERT: A 34 ASN cc_start: 0.6062 (m110) cc_final: 0.5786 (m110) REVERT: A 37 GLU cc_start: 0.6383 (pt0) cc_final: 0.6130 (pt0) REVERT: A 58 HIS cc_start: 0.7531 (m90) cc_final: 0.6861 (m90) REVERT: A 78 LYS cc_start: 0.7099 (ptpt) cc_final: 0.6581 (pttm) REVERT: A 81 ASP cc_start: 0.5545 (m-30) cc_final: 0.5213 (m-30) REVERT: A 190 LYS cc_start: 0.7637 (mttt) cc_final: 0.7389 (mtmm) REVERT: A 237 GLN cc_start: 0.6130 (mm-40) cc_final: 0.5449 (tm-30) REVERT: A 357 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7753 (pm20) REVERT: A 392 ASN cc_start: 0.7520 (m-40) cc_final: 0.7190 (m-40) REVERT: A 474 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7044 (mp0) REVERT: A 499 TYR cc_start: 0.7518 (t80) cc_final: 0.7151 (t80) REVERT: A 509 ASP cc_start: 0.7473 (m-30) cc_final: 0.6515 (p0) REVERT: A 543 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6403 (mtm110) REVERT: A 617 LEU cc_start: 0.7777 (mp) cc_final: 0.7541 (mm) REVERT: A 624 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7255 (m) REVERT: B 80 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6545 (tptt) REVERT: B 114 ILE cc_start: 0.7652 (tp) cc_final: 0.7448 (tp) REVERT: B 128 ARG cc_start: 0.6704 (mtp180) cc_final: 0.6366 (ttp-170) REVERT: B 163 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6896 (m-70) REVERT: B 169 SER cc_start: 0.8026 (t) cc_final: 0.7420 (p) REVERT: B 184 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5515 (mm-30) REVERT: C 56 LEU cc_start: 0.7650 (mt) cc_final: 0.7424 (mt) REVERT: C 140 ASP cc_start: 0.6272 (m-30) cc_final: 0.5933 (m-30) REVERT: D 49 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7350 (pt0) REVERT: D 54 LYS cc_start: 0.6749 (ttpt) cc_final: 0.6279 (ttmm) REVERT: D 59 ARG cc_start: 0.5864 (ttm170) cc_final: 0.5258 (tmt170) REVERT: D 85 TRP cc_start: 0.7480 (m-10) cc_final: 0.7183 (m-10) outliers start: 40 outliers final: 17 residues processed: 207 average time/residue: 0.9332 time to fit residues: 212.6900 Evaluate side-chains 165 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 81 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 531 ASN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 454 GLN B 464 GLN C 58 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11180 Z= 0.205 Angle : 0.620 10.055 15243 Z= 0.298 Chirality : 0.044 0.406 1830 Planarity : 0.004 0.060 1845 Dihedral : 9.789 111.573 2074 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.91 % Allowed : 13.15 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1322 helix: 0.92 (0.19), residues: 735 sheet: -0.92 (0.47), residues: 122 loop : -2.09 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 209 HIS 0.007 0.001 HIS C 58 PHE 0.035 0.002 PHE A 302 TYR 0.014 0.002 TYR D 47 ARG 0.007 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 150 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6440 (tp) REVERT: A 34 ASN cc_start: 0.6154 (m110) cc_final: 0.5830 (m110) REVERT: A 37 GLU cc_start: 0.6703 (pt0) cc_final: 0.6392 (pt0) REVERT: A 63 GLN cc_start: 0.7204 (tt0) cc_final: 0.6997 (tp40) REVERT: A 78 LYS cc_start: 0.7367 (ptpt) cc_final: 0.6827 (ptmm) REVERT: A 231 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5808 (mmp) REVERT: A 357 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7676 (pm20) REVERT: A 392 ASN cc_start: 0.7484 (m-40) cc_final: 0.6868 (m-40) REVERT: A 396 ASP cc_start: 0.8344 (m-30) cc_final: 0.8117 (m-30) REVERT: A 543 ARG cc_start: 0.6930 (mtm180) cc_final: 0.6660 (mtm-85) REVERT: A 598 ASP cc_start: 0.7243 (p0) cc_final: 0.6561 (p0) REVERT: A 617 LEU cc_start: 0.7722 (mp) cc_final: 0.7513 (mm) REVERT: B 128 ARG cc_start: 0.6681 (mtp180) cc_final: 0.6201 (ttp-170) REVERT: B 130 LEU cc_start: 0.6971 (mm) cc_final: 0.6769 (mm) REVERT: B 163 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6889 (m-70) REVERT: B 165 TRP cc_start: 0.7823 (t60) cc_final: 0.7512 (t-100) REVERT: B 380 LYS cc_start: 0.7399 (mttm) cc_final: 0.6876 (mptt) REVERT: C 31 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.6112 (mtt180) REVERT: C 62 ARG cc_start: 0.5662 (mmt90) cc_final: 0.5272 (ttp80) REVERT: C 121 SER cc_start: 0.7085 (OUTLIER) cc_final: 0.6834 (p) REVERT: C 140 ASP cc_start: 0.6349 (m-30) cc_final: 0.6073 (m-30) REVERT: C 186 ARG cc_start: 0.7529 (ptp-170) cc_final: 0.7271 (ptp-170) REVERT: D 49 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7295 (pt0) REVERT: D 59 ARG cc_start: 0.6136 (ttm170) cc_final: 0.5414 (tmt170) REVERT: D 81 TYR cc_start: 0.6424 (m-10) cc_final: 0.6205 (m-10) REVERT: D 84 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6125 (mtm180) REVERT: D 85 TRP cc_start: 0.7412 (m-10) cc_final: 0.7056 (m-10) outliers start: 56 outliers final: 22 residues processed: 190 average time/residue: 0.9660 time to fit residues: 201.6259 Evaluate side-chains 162 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 126 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 113 optimal weight: 0.0060 chunk 34 optimal weight: 3.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11180 Z= 0.174 Angle : 0.564 10.816 15243 Z= 0.271 Chirality : 0.042 0.332 1830 Planarity : 0.004 0.040 1845 Dihedral : 9.079 103.752 2074 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 4.03 % Allowed : 16.39 % Favored : 79.58 % 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: 0.14 (0.24), residues: 1322 helix: 1.42 (0.20), residues: 741 sheet: -0.89 (0.47), residues: 122 loop : -1.88 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.005 0.001 HIS C 197 PHE 0.030 0.001 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6644 (pt0) cc_final: 0.6373 (pt0) REVERT: A 357 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7694 (pm20) REVERT: A 392 ASN cc_start: 0.7360 (m-40) cc_final: 0.7076 (m-40) REVERT: A 543 ARG cc_start: 0.6878 (mtm180) cc_final: 0.6632 (mtm-85) REVERT: A 587 GLN cc_start: 0.7405 (mm110) cc_final: 0.7169 (mp10) REVERT: A 598 ASP cc_start: 0.7167 (p0) cc_final: 0.6456 (p0) REVERT: A 624 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7289 (m) REVERT: B 128 ARG cc_start: 0.6692 (mtp180) cc_final: 0.6261 (ttp-170) REVERT: B 163 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6898 (m-70) REVERT: B 165 TRP cc_start: 0.7908 (t60) cc_final: 0.7534 (t-100) REVERT: B 380 LYS cc_start: 0.7447 (mttm) cc_final: 0.6860 (mptt) REVERT: B 390 SER cc_start: 0.7398 (m) cc_final: 0.7168 (p) REVERT: C 62 ARG cc_start: 0.5812 (mmt90) cc_final: 0.5448 (ttp80) REVERT: C 117 MET cc_start: 0.7670 (mtm) cc_final: 0.7408 (mtt) REVERT: C 186 ARG cc_start: 0.7467 (ptp-170) cc_final: 0.7137 (ptp-170) REVERT: D 59 ARG cc_start: 0.6256 (ttm170) cc_final: 0.5510 (tmt170) REVERT: D 81 TYR cc_start: 0.6567 (m-10) cc_final: 0.6272 (m-80) REVERT: D 84 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6235 (mtm180) REVERT: D 85 TRP cc_start: 0.7442 (m-10) cc_final: 0.6975 (m-10) outliers start: 46 outliers final: 20 residues processed: 177 average time/residue: 0.9711 time to fit residues: 189.0036 Evaluate side-chains 151 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 255 ASN A 393 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11180 Z= 0.280 Angle : 0.634 11.807 15243 Z= 0.305 Chirality : 0.045 0.505 1830 Planarity : 0.004 0.040 1845 Dihedral : 8.848 83.563 2074 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.37 % Rotamer: Outliers : 4.65 % Allowed : 17.09 % Favored : 78.26 % 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: 0.16 (0.23), residues: 1322 helix: 1.45 (0.20), residues: 734 sheet: -0.77 (0.46), residues: 129 loop : -1.90 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 209 HIS 0.007 0.002 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.019 0.002 TYR C 218 ARG 0.004 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6666 (pt0) cc_final: 0.6278 (pt0) REVERT: A 78 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6656 (ptmm) REVERT: A 249 ASP cc_start: 0.6777 (t0) cc_final: 0.6010 (p0) REVERT: A 357 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7731 (pm20) REVERT: A 392 ASN cc_start: 0.7274 (m-40) cc_final: 0.6880 (m-40) REVERT: A 482 ASP cc_start: 0.6867 (m-30) cc_final: 0.6463 (m-30) REVERT: A 543 ARG cc_start: 0.6814 (mtm180) cc_final: 0.6568 (mtm-85) REVERT: A 598 ASP cc_start: 0.7082 (p0) cc_final: 0.6388 (p0) REVERT: A 624 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7606 (m) REVERT: A 655 ASP cc_start: 0.5831 (t0) cc_final: 0.5079 (t70) REVERT: A 677 PHE cc_start: 0.6668 (m-80) cc_final: 0.6216 (m-10) REVERT: B 128 ARG cc_start: 0.6645 (mtp180) cc_final: 0.6183 (ttp-170) REVERT: B 163 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6890 (m-70) REVERT: B 165 TRP cc_start: 0.7991 (t60) cc_final: 0.7554 (t-100) REVERT: B 194 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7092 (p0) REVERT: B 390 SER cc_start: 0.7310 (m) cc_final: 0.7075 (p) REVERT: C 62 ARG cc_start: 0.5872 (mmt90) cc_final: 0.5505 (ttp80) REVERT: C 121 SER cc_start: 0.7308 (OUTLIER) cc_final: 0.7101 (p) REVERT: C 186 ARG cc_start: 0.7493 (ptp-170) cc_final: 0.7253 (ptm-80) REVERT: C 236 LEU cc_start: 0.7885 (mm) cc_final: 0.7631 (tp) REVERT: D 59 ARG cc_start: 0.6490 (ttm170) cc_final: 0.5596 (tmt170) REVERT: D 84 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6269 (mtm180) REVERT: D 85 TRP cc_start: 0.7335 (m-10) cc_final: 0.6931 (m-10) outliers start: 53 outliers final: 23 residues processed: 179 average time/residue: 0.9770 time to fit residues: 192.1547 Evaluate side-chains 155 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 126 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 393 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11180 Z= 0.192 Angle : 0.585 11.130 15243 Z= 0.279 Chirality : 0.043 0.288 1830 Planarity : 0.003 0.040 1845 Dihedral : 8.321 72.695 2074 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 3.42 % Allowed : 18.67 % Favored : 77.91 % 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: 0.37 (0.24), residues: 1322 helix: 1.61 (0.20), residues: 736 sheet: -0.57 (0.46), residues: 125 loop : -1.82 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 74 HIS 0.005 0.001 HIS A 553 PHE 0.031 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6685 (pt0) cc_final: 0.6291 (pt0) REVERT: A 78 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6689 (ptmm) REVERT: A 249 ASP cc_start: 0.6947 (t0) cc_final: 0.6324 (p0) REVERT: A 357 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7742 (pm20) REVERT: A 392 ASN cc_start: 0.7222 (m-40) cc_final: 0.6862 (m-40) REVERT: A 482 ASP cc_start: 0.6928 (m-30) cc_final: 0.6556 (m-30) REVERT: A 507 PHE cc_start: 0.8163 (m-80) cc_final: 0.7894 (m-80) REVERT: A 543 ARG cc_start: 0.6802 (mtm180) cc_final: 0.6562 (mtm-85) REVERT: A 598 ASP cc_start: 0.7078 (p0) cc_final: 0.6659 (p0) REVERT: A 624 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7537 (m) REVERT: A 655 ASP cc_start: 0.5663 (t0) cc_final: 0.4934 (t70) REVERT: A 677 PHE cc_start: 0.6702 (m-80) cc_final: 0.6125 (m-10) REVERT: B 165 TRP cc_start: 0.7978 (t60) cc_final: 0.7558 (t60) REVERT: B 194 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B 390 SER cc_start: 0.7340 (m) cc_final: 0.7109 (p) REVERT: C 62 ARG cc_start: 0.5884 (mmt90) cc_final: 0.5506 (ttp80) REVERT: C 186 ARG cc_start: 0.7448 (ptp-170) cc_final: 0.7094 (ptp-170) REVERT: D 59 ARG cc_start: 0.6536 (ttm170) cc_final: 0.5655 (mmt180) REVERT: D 84 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6522 (mtm180) REVERT: D 85 TRP cc_start: 0.7472 (m-10) cc_final: 0.7060 (m-10) outliers start: 39 outliers final: 15 residues processed: 163 average time/residue: 0.9866 time to fit residues: 176.7532 Evaluate side-chains 148 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11180 Z= 0.189 Angle : 0.569 10.918 15243 Z= 0.273 Chirality : 0.043 0.299 1830 Planarity : 0.003 0.040 1845 Dihedral : 7.815 72.185 2071 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 3.77 % Allowed : 19.19 % Favored : 77.04 % 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: 0.52 (0.24), residues: 1322 helix: 1.75 (0.20), residues: 736 sheet: -0.60 (0.45), residues: 125 loop : -1.76 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.005 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.003 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6732 (pt0) cc_final: 0.6334 (pt0) REVERT: A 249 ASP cc_start: 0.6998 (t0) cc_final: 0.6406 (p0) REVERT: A 392 ASN cc_start: 0.7175 (m-40) cc_final: 0.6830 (m-40) REVERT: A 482 ASP cc_start: 0.6982 (m-30) cc_final: 0.6630 (m-30) REVERT: A 543 ARG cc_start: 0.6784 (mtm180) cc_final: 0.6546 (mtm-85) REVERT: A 587 GLN cc_start: 0.7528 (mm110) cc_final: 0.7189 (mp10) REVERT: A 598 ASP cc_start: 0.7274 (p0) cc_final: 0.6565 (p0) REVERT: A 624 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7503 (m) REVERT: A 655 ASP cc_start: 0.5623 (t0) cc_final: 0.4873 (t70) REVERT: A 677 PHE cc_start: 0.6731 (m-80) cc_final: 0.6167 (m-10) REVERT: B 128 ARG cc_start: 0.6851 (ttt180) cc_final: 0.6648 (ttp-170) REVERT: B 130 LEU cc_start: 0.6985 (mm) cc_final: 0.6773 (mm) REVERT: B 147 THR cc_start: 0.6242 (m) cc_final: 0.5996 (m) REVERT: B 165 TRP cc_start: 0.7976 (t60) cc_final: 0.7523 (t60) REVERT: B 194 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6966 (p0) REVERT: B 390 SER cc_start: 0.7361 (m) cc_final: 0.7141 (p) REVERT: B 401 SER cc_start: 0.6943 (t) cc_final: 0.6663 (p) REVERT: C 62 ARG cc_start: 0.5853 (mmt90) cc_final: 0.5523 (ttp80) REVERT: D 59 ARG cc_start: 0.6550 (ttm170) cc_final: 0.5631 (mmt180) REVERT: D 84 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6509 (mtm180) REVERT: D 85 TRP cc_start: 0.7494 (m-10) cc_final: 0.7084 (m-10) outliers start: 43 outliers final: 21 residues processed: 169 average time/residue: 0.9459 time to fit residues: 176.6660 Evaluate side-chains 154 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11180 Z= 0.208 Angle : 0.581 10.817 15243 Z= 0.280 Chirality : 0.042 0.280 1830 Planarity : 0.004 0.042 1845 Dihedral : 7.552 72.096 2071 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.98 % Allowed : 20.77 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1322 helix: 1.74 (0.20), residues: 737 sheet: -0.66 (0.45), residues: 125 loop : -1.74 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.005 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6833 (pt0) cc_final: 0.6426 (pt0) REVERT: A 78 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6643 (ptmm) REVERT: A 237 GLN cc_start: 0.6349 (tp40) cc_final: 0.5887 (mm110) REVERT: A 249 ASP cc_start: 0.6977 (t0) cc_final: 0.6381 (p0) REVERT: A 253 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7867 (t70) REVERT: A 392 ASN cc_start: 0.7121 (m-40) cc_final: 0.6769 (m-40) REVERT: A 543 ARG cc_start: 0.6686 (mtm180) cc_final: 0.6452 (mtm-85) REVERT: A 587 GLN cc_start: 0.7574 (mm110) cc_final: 0.6960 (mp10) REVERT: A 598 ASP cc_start: 0.7214 (p0) cc_final: 0.6501 (p0) REVERT: A 624 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7546 (m) REVERT: A 655 ASP cc_start: 0.5664 (t0) cc_final: 0.4896 (t70) REVERT: A 677 PHE cc_start: 0.6763 (m-80) cc_final: 0.6207 (m-10) REVERT: B 130 LEU cc_start: 0.6934 (mm) cc_final: 0.6732 (mm) REVERT: B 165 TRP cc_start: 0.7978 (t60) cc_final: 0.7525 (t60) REVERT: B 194 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6923 (p0) REVERT: B 390 SER cc_start: 0.7361 (m) cc_final: 0.7145 (p) REVERT: B 401 SER cc_start: 0.6933 (t) cc_final: 0.6650 (p) REVERT: C 62 ARG cc_start: 0.6077 (mmt90) cc_final: 0.5755 (ttp80) REVERT: D 59 ARG cc_start: 0.6602 (ttm170) cc_final: 0.5788 (mmt180) REVERT: D 84 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6634 (mtm180) REVERT: D 85 TRP cc_start: 0.7486 (m-10) cc_final: 0.7137 (m-10) outliers start: 34 outliers final: 24 residues processed: 167 average time/residue: 0.9971 time to fit residues: 182.5889 Evaluate side-chains 163 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11180 Z= 0.222 Angle : 0.586 10.664 15243 Z= 0.283 Chirality : 0.043 0.279 1830 Planarity : 0.004 0.041 1845 Dihedral : 7.263 65.355 2071 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 3.51 % Allowed : 20.60 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1322 helix: 1.77 (0.20), residues: 737 sheet: -0.86 (0.44), residues: 129 loop : -1.72 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 244 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.002 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.008 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6831 (pt0) cc_final: 0.6431 (pt0) REVERT: A 156 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 237 GLN cc_start: 0.6351 (tp40) cc_final: 0.5903 (mm110) REVERT: A 249 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6414 (p0) REVERT: A 392 ASN cc_start: 0.7125 (m-40) cc_final: 0.6792 (m-40) REVERT: A 507 PHE cc_start: 0.8297 (m-80) cc_final: 0.8031 (m-80) REVERT: A 543 ARG cc_start: 0.6729 (mtm180) cc_final: 0.6479 (mtm-85) REVERT: A 587 GLN cc_start: 0.7578 (mm110) cc_final: 0.6957 (mp10) REVERT: A 598 ASP cc_start: 0.7261 (p0) cc_final: 0.6562 (p0) REVERT: A 624 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7574 (m) REVERT: A 655 ASP cc_start: 0.5707 (t0) cc_final: 0.4933 (t70) REVERT: A 677 PHE cc_start: 0.6746 (m-80) cc_final: 0.6161 (m-10) REVERT: B 130 LEU cc_start: 0.6950 (mm) cc_final: 0.6750 (mm) REVERT: B 147 THR cc_start: 0.6273 (m) cc_final: 0.5951 (m) REVERT: B 165 TRP cc_start: 0.7961 (t60) cc_final: 0.7548 (t60) REVERT: B 184 GLU cc_start: 0.5658 (mm-30) cc_final: 0.5330 (mt-10) REVERT: B 194 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6929 (p0) REVERT: B 390 SER cc_start: 0.7361 (m) cc_final: 0.7142 (p) REVERT: C 62 ARG cc_start: 0.6107 (mmt90) cc_final: 0.5743 (ttp80) REVERT: D 59 ARG cc_start: 0.6622 (ttm170) cc_final: 0.5731 (mmt180) REVERT: D 85 TRP cc_start: 0.7530 (m-10) cc_final: 0.7182 (m-10) outliers start: 40 outliers final: 25 residues processed: 168 average time/residue: 0.9665 time to fit residues: 178.7191 Evaluate side-chains 162 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11180 Z= 0.231 Angle : 0.598 10.497 15243 Z= 0.288 Chirality : 0.043 0.276 1830 Planarity : 0.004 0.042 1845 Dihedral : 6.944 56.349 2071 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.89 % Allowed : 21.21 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1322 helix: 1.74 (0.20), residues: 737 sheet: -0.84 (0.44), residues: 127 loop : -1.71 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 244 HIS 0.005 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.012 0.001 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6835 (pt0) cc_final: 0.6434 (pt0) REVERT: A 156 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: A 237 GLN cc_start: 0.6215 (tp40) cc_final: 0.5781 (mm110) REVERT: A 249 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6402 (p0) REVERT: A 392 ASN cc_start: 0.7202 (m-40) cc_final: 0.6817 (m110) REVERT: A 543 ARG cc_start: 0.6717 (mtm180) cc_final: 0.6466 (mtm-85) REVERT: A 587 GLN cc_start: 0.7581 (mm110) cc_final: 0.6967 (mp10) REVERT: A 598 ASP cc_start: 0.7225 (p0) cc_final: 0.6533 (p0) REVERT: A 624 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7572 (m) REVERT: A 655 ASP cc_start: 0.5907 (t0) cc_final: 0.5120 (t70) REVERT: A 677 PHE cc_start: 0.6741 (m-80) cc_final: 0.6183 (m-10) REVERT: B 147 THR cc_start: 0.6318 (m) cc_final: 0.6107 (m) REVERT: B 165 TRP cc_start: 0.7970 (t60) cc_final: 0.7431 (t60) REVERT: B 194 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6924 (p0) REVERT: B 390 SER cc_start: 0.7363 (m) cc_final: 0.7144 (p) REVERT: C 62 ARG cc_start: 0.6277 (mmt90) cc_final: 0.5938 (ttp80) REVERT: C 185 ARG cc_start: 0.6629 (mtt180) cc_final: 0.6257 (ttm-80) REVERT: C 187 TYR cc_start: 0.7866 (m-80) cc_final: 0.7331 (m-80) REVERT: D 59 ARG cc_start: 0.6624 (ttm170) cc_final: 0.5709 (mmt180) REVERT: D 85 TRP cc_start: 0.7529 (m-10) cc_final: 0.7174 (m-10) outliers start: 33 outliers final: 20 residues processed: 155 average time/residue: 0.9162 time to fit residues: 156.6490 Evaluate side-chains 151 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103499 restraints weight = 14330.971| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.30 r_work: 0.3134 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11180 Z= 0.175 Angle : 0.573 10.360 15243 Z= 0.276 Chirality : 0.042 0.276 1830 Planarity : 0.004 0.061 1845 Dihedral : 6.778 58.851 2069 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.37 % Allowed : 22.17 % Favored : 75.46 % 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: 0.57 (0.24), residues: 1322 helix: 1.81 (0.20), residues: 738 sheet: -0.90 (0.43), residues: 129 loop : -1.69 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 36 HIS 0.006 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.011 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3916.57 seconds wall clock time: 69 minutes 22.30 seconds (4162.30 seconds total)