Starting phenix.real_space_refine on Fri Mar 15 15:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/03_2024/7ktp_23025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/03_2024/7ktp_23025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/03_2024/7ktp_23025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/03_2024/7ktp_23025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/03_2024/7ktp_23025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktp_23025/03_2024/7ktp_23025.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 88 5.16 5 C 7585 2.51 5 N 2129 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12008 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2932 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 15, 'TRANS': 381} Chain breaks: 9 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3054 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 939 SG CYS A 302 30.674 93.245 115.304 0.99110.70 S ATOM 985 SG CYS A 307 27.984 95.013 113.853 0.87115.67 S ATOM 1591 SG CYS A 531 18.407 73.629 116.676 1.00169.00 S ATOM 1684 SG CYS A 544 20.797 75.718 113.378 1.00139.90 S ATOM 1734 SG CYS A 550 21.476 75.101 118.290 1.00148.49 S ATOM 1591 SG CYS A 531 18.407 73.629 116.676 1.00169.00 S ATOM 1684 SG CYS A 544 20.797 75.718 113.378 1.00139.90 S ATOM 1534 SG CYS A 524 17.395 79.645 115.870 1.00134.37 S ATOM 1719 SG CYS A 548 20.534 78.895 117.300 1.00137.34 S ATOM 1819 SG CYS A 561 38.830 72.036 108.448 1.00170.41 S ATOM 1973 SG CYS A 581 38.994 75.630 106.850 1.00146.47 S ATOM 2031 SG CYS A 589 42.140 74.320 110.087 1.00177.73 S ATOM 1819 SG CYS A 561 38.830 72.036 108.448 1.00170.41 S ATOM 1867 SG CYS A 567 40.775 73.315 104.723 1.00172.65 S ATOM 1906 SG CYS A 572 37.313 70.956 104.487 1.00183.12 S ATOM 1867 SG CYS A 567 40.775 73.315 104.723 1.00172.65 S Time building chain proxies: 6.58, per 1000 atoms: 0.55 Number of scatterers: 12008 At special positions: 0 Unit cell: (86.4, 166.05, 167.4, 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) Zn 7 29.99 S 88 16.00 O 2199 8.00 N 2129 7.00 C 7585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 310 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 544 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 531 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 572 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 567 " 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 23 sheets defined 20.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 34 through 62 removed outlier: 3.903A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.970A pdb=" N VAL A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.613A pdb=" N LYS A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.721A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.051A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.519A pdb=" N ALA A 688 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.621A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 343 " --> pdb=" O ILE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.749A pdb=" N HIS C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.718A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.005A pdb=" N LYS C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 131' Processing helix chain 'C' and resid 136 through 145 removed outlier: 4.367A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.560A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.924A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 624 Processing helix chain 'C' and resid 631 through 649 removed outlier: 4.162A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.645A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.516A pdb=" N ILE C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.893A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.101A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 5.856A pdb=" N SER A 115 " --> pdb=" O GLY A 682 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.552A pdb=" N PHE A 121 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.985A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.172A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.284A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 116 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 100 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 114 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.537A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 167 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.683A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.314A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 234 Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 211 removed outlier: 7.020A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS C 210 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 184 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 440 through 441 removed outlier: 4.531A pdb=" N GLN C 440 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 432 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE C 429 " --> pdb=" O ILE C 487 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 489 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 431 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 491 " --> pdb=" O GLN C 431 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 486 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 479 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 525 through 527 removed outlier: 3.689A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.796A pdb=" N TYR C 565 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.274A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AC2, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.590A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.785A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.956A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.042A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1104 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: 3.70 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3943 1.34 - 1.46: 2770 1.46 - 1.58: 5448 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 12282 Sorted by residual: bond pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.25e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" CA ILE B 290 " pdb=" CB ILE B 290 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.07e+00 bond pdb=" CA ARG C 196 " pdb=" C ARG C 196 " ideal model delta sigma weight residual 1.522 1.542 -0.019 1.36e-02 5.41e+03 2.04e+00 bond pdb=" CB PHE D 223 " pdb=" CG PHE D 223 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.95e+00 ... (remaining 12277 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.00: 407 107.00 - 113.76: 6688 113.76 - 120.53: 4629 120.53 - 127.29: 4738 127.29 - 134.06: 190 Bond angle restraints: 16652 Sorted by residual: angle pdb=" N ILE C 627 " pdb=" CA ILE C 627 " pdb=" C ILE C 627 " ideal model delta sigma weight residual 112.96 109.09 3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N THR D 28 " pdb=" CA THR D 28 " pdb=" C THR D 28 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.81e+00 angle pdb=" CA THR D 28 " pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 118.44 123.03 -4.59 1.59e+00 3.96e-01 8.33e+00 angle pdb=" N ARG C 196 " pdb=" CA ARG C 196 " pdb=" C ARG C 196 " ideal model delta sigma weight residual 111.71 115.02 -3.31 1.15e+00 7.56e-01 8.31e+00 angle pdb=" CA GLU C 493 " pdb=" CB GLU C 493 " pdb=" CG GLU C 493 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 ... (remaining 16647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6839 17.15 - 34.30: 417 34.30 - 51.45: 58 51.45 - 68.60: 15 68.60 - 85.75: 11 Dihedral angle restraints: 7340 sinusoidal: 2812 harmonic: 4528 Sorted by residual: dihedral pdb=" CA THR D 297 " pdb=" C THR D 297 " pdb=" N VAL D 298 " pdb=" CA VAL D 298 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP C 588 " pdb=" C ASP C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TYR B 244 " pdb=" C TYR B 244 " pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1163 0.036 - 0.072: 460 0.072 - 0.108: 122 0.108 - 0.144: 75 0.144 - 0.180: 13 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA THR D 28 " pdb=" N THR D 28 " pdb=" C THR D 28 " pdb=" CB THR D 28 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE B 228 " pdb=" N ILE B 228 " pdb=" C ILE B 228 " pdb=" CB ILE B 228 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1830 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO D 29 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 195 " 0.009 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LYS C 195 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS C 195 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 86 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 87 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " 0.023 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1275 2.76 - 3.29: 11705 3.29 - 3.83: 18342 3.83 - 4.36: 21638 4.36 - 4.90: 38319 Nonbonded interactions: 91279 Sorted by model distance: nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.221 2.440 nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.281 2.440 nonbonded pdb=" O LEU C 100 " pdb=" ND2 ASN C 104 " model vdw 2.291 2.520 nonbonded pdb=" O ARG C 427 " pdb=" N ALA C 485 " model vdw 2.309 2.520 nonbonded pdb=" O ALA A 591 " pdb=" NH2 ARG A 609 " model vdw 2.320 2.520 ... (remaining 91274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.970 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.180 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12282 Z= 0.304 Angle : 0.725 8.935 16652 Z= 0.382 Chirality : 0.047 0.180 1833 Planarity : 0.004 0.047 2152 Dihedral : 11.993 85.753 4380 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.17), residues: 1508 helix: -1.87 (0.23), residues: 267 sheet: -3.01 (0.23), residues: 324 loop : -3.04 (0.16), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 345 HIS 0.004 0.001 HIS B 213 PHE 0.022 0.001 PHE C 86 TYR 0.015 0.001 TYR B 244 ARG 0.003 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8472 (tp30) REVERT: A 115 SER cc_start: 0.8523 (m) cc_final: 0.8292 (t) REVERT: A 607 ILE cc_start: 0.8831 (mp) cc_final: 0.8549 (tt) REVERT: A 613 LYS cc_start: 0.7632 (mmtt) cc_final: 0.6512 (mmmm) REVERT: B 94 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8513 (mp10) REVERT: B 104 HIS cc_start: 0.8659 (m-70) cc_final: 0.8389 (p-80) REVERT: B 122 THR cc_start: 0.8025 (p) cc_final: 0.6581 (p) REVERT: B 124 TYR cc_start: 0.7878 (m-80) cc_final: 0.7331 (m-10) REVERT: B 152 TRP cc_start: 0.8534 (m100) cc_final: 0.8331 (m100) REVERT: B 157 ASN cc_start: 0.9515 (m-40) cc_final: 0.9133 (p0) REVERT: B 182 CYS cc_start: 0.6684 (t) cc_final: 0.6334 (t) REVERT: B 196 LEU cc_start: 0.9096 (mt) cc_final: 0.8697 (mt) REVERT: B 197 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7871 (mmtp) REVERT: B 217 LEU cc_start: 0.9330 (tp) cc_final: 0.9119 (tp) REVERT: B 225 LEU cc_start: 0.8970 (tt) cc_final: 0.8519 (pt) REVERT: B 228 ILE cc_start: 0.9400 (mt) cc_final: 0.9074 (mm) REVERT: B 240 LEU cc_start: 0.9182 (mt) cc_final: 0.8667 (tp) REVERT: B 252 MET cc_start: 0.9172 (mmm) cc_final: 0.8895 (mmm) REVERT: B 263 TRP cc_start: 0.7467 (m100) cc_final: 0.6914 (m100) REVERT: B 271 MET cc_start: 0.9385 (mmm) cc_final: 0.9129 (mmt) REVERT: B 291 SER cc_start: 0.9075 (t) cc_final: 0.8532 (p) REVERT: B 294 ILE cc_start: 0.8987 (mm) cc_final: 0.8355 (mm) REVERT: B 314 TRP cc_start: 0.8026 (m100) cc_final: 0.6473 (m100) REVERT: B 325 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8473 (mp0) REVERT: B 330 CYS cc_start: 0.8529 (t) cc_final: 0.7373 (p) REVERT: B 331 TRP cc_start: 0.8662 (p-90) cc_final: 0.7691 (p-90) REVERT: C 80 GLN cc_start: 0.5374 (pt0) cc_final: 0.4286 (tp40) REVERT: C 111 LEU cc_start: 0.9475 (mt) cc_final: 0.9041 (mp) REVERT: C 574 LEU cc_start: 0.8262 (tp) cc_final: 0.7976 (tp) REVERT: C 598 THR cc_start: 0.9570 (t) cc_final: 0.9345 (p) REVERT: C 615 LYS cc_start: 0.9203 (pttt) cc_final: 0.8987 (pttp) REVERT: C 659 HIS cc_start: 0.9007 (t70) cc_final: 0.8779 (t-90) REVERT: C 660 LEU cc_start: 0.9563 (mt) cc_final: 0.9211 (mt) REVERT: C 663 MET cc_start: 0.8496 (ptp) cc_final: 0.8192 (ptt) REVERT: D 13 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6378 (mt-10) REVERT: D 28 THR cc_start: 0.9080 (t) cc_final: 0.8614 (p) REVERT: D 45 LEU cc_start: 0.7392 (mt) cc_final: 0.7162 (mm) REVERT: D 48 GLN cc_start: 0.8469 (tt0) cc_final: 0.8135 (pm20) REVERT: D 115 ILE cc_start: 0.6654 (mm) cc_final: 0.5289 (mm) REVERT: D 261 ASN cc_start: 0.8575 (t0) cc_final: 0.7655 (p0) REVERT: D 275 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8001 (mp0) REVERT: D 313 PHE cc_start: 0.8722 (m-80) cc_final: 0.7849 (m-10) REVERT: D 367 LEU cc_start: 0.9154 (tp) cc_final: 0.8695 (tt) REVERT: D 403 GLN cc_start: 0.8623 (tt0) cc_final: 0.8253 (tm-30) REVERT: D 404 MET cc_start: 0.8197 (ptp) cc_final: 0.7933 (ptp) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2802 time to fit residues: 152.6389 Evaluate side-chains 224 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 690 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 235 HIS ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 HIS D 27 ASN D 267 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12282 Z= 0.215 Angle : 0.608 6.899 16652 Z= 0.318 Chirality : 0.045 0.236 1833 Planarity : 0.004 0.065 2152 Dihedral : 4.424 23.205 1639 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.19), residues: 1508 helix: -0.34 (0.28), residues: 292 sheet: -2.14 (0.24), residues: 356 loop : -2.43 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 218 HIS 0.009 0.001 HIS A 313 PHE 0.020 0.002 PHE A 294 TYR 0.020 0.002 TYR A 659 ARG 0.013 0.001 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8762 (tp30) REVERT: A 62 LYS cc_start: 0.9556 (pttm) cc_final: 0.9347 (pttp) REVERT: A 553 ASP cc_start: 0.8436 (t0) cc_final: 0.8160 (t0) REVERT: A 651 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9220 (tp30) REVERT: A 681 LYS cc_start: 0.8683 (mttt) cc_final: 0.8400 (mtmm) REVERT: A 702 MET cc_start: 0.7667 (ptt) cc_final: 0.7417 (ptt) REVERT: A 707 HIS cc_start: 0.7910 (m-70) cc_final: 0.7361 (m-70) REVERT: A 717 ILE cc_start: 0.6746 (mt) cc_final: 0.6544 (mt) REVERT: B 122 THR cc_start: 0.8026 (p) cc_final: 0.7117 (p) REVERT: B 124 TYR cc_start: 0.8406 (m-80) cc_final: 0.8039 (m-10) REVERT: B 152 TRP cc_start: 0.8970 (m100) cc_final: 0.8640 (m100) REVERT: B 157 ASN cc_start: 0.9498 (m-40) cc_final: 0.9138 (p0) REVERT: B 198 PHE cc_start: 0.8710 (m-80) cc_final: 0.8335 (m-80) REVERT: B 218 TRP cc_start: 0.9307 (m-90) cc_final: 0.8509 (m-90) REVERT: B 221 GLN cc_start: 0.9041 (mm110) cc_final: 0.8799 (mm-40) REVERT: B 225 LEU cc_start: 0.9456 (tt) cc_final: 0.8941 (pt) REVERT: B 252 MET cc_start: 0.9331 (mmm) cc_final: 0.8865 (mmm) REVERT: B 263 TRP cc_start: 0.7857 (m100) cc_final: 0.7199 (m100) REVERT: B 291 SER cc_start: 0.9273 (t) cc_final: 0.8911 (p) REVERT: B 294 ILE cc_start: 0.8774 (mm) cc_final: 0.8491 (mm) REVERT: B 331 TRP cc_start: 0.8796 (p-90) cc_final: 0.7617 (p-90) REVERT: B 362 ASP cc_start: 0.9233 (m-30) cc_final: 0.8949 (p0) REVERT: B 370 MET cc_start: 0.8334 (mtm) cc_final: 0.7909 (ptp) REVERT: B 377 LEU cc_start: 0.8686 (tt) cc_final: 0.8150 (tp) REVERT: C 111 LEU cc_start: 0.9409 (mt) cc_final: 0.9109 (mp) REVERT: C 117 TYR cc_start: 0.6924 (p90) cc_final: 0.6653 (p90) REVERT: C 574 LEU cc_start: 0.8541 (tp) cc_final: 0.7366 (tp) REVERT: C 595 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8814 (mmmm) REVERT: C 615 LYS cc_start: 0.9164 (pttt) cc_final: 0.8824 (pttp) REVERT: C 638 LEU cc_start: 0.9263 (mt) cc_final: 0.8515 (mt) REVERT: C 684 MET cc_start: 0.8433 (mpp) cc_final: 0.8106 (mpp) REVERT: D 28 THR cc_start: 0.9161 (t) cc_final: 0.8786 (t) REVERT: D 36 MET cc_start: 0.8652 (tpt) cc_final: 0.8294 (tmm) REVERT: D 252 LEU cc_start: 0.9272 (mp) cc_final: 0.9060 (mp) REVERT: D 253 MET cc_start: 0.4583 (mpp) cc_final: 0.4359 (mpp) REVERT: D 275 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8005 (mp0) REVERT: D 367 LEU cc_start: 0.9170 (tp) cc_final: 0.8775 (tt) REVERT: D 399 MET cc_start: 0.9366 (tmm) cc_final: 0.8421 (tmm) REVERT: D 403 GLN cc_start: 0.8400 (tt0) cc_final: 0.8045 (tm-30) REVERT: D 404 MET cc_start: 0.8949 (ptp) cc_final: 0.8597 (ptp) outliers start: 3 outliers final: 1 residues processed: 252 average time/residue: 0.2367 time to fit residues: 87.9646 Evaluate side-chains 184 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 138 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN C 88 GLN C 527 HIS D 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12282 Z= 0.145 Angle : 0.520 7.059 16652 Z= 0.271 Chirality : 0.043 0.214 1833 Planarity : 0.003 0.035 2152 Dihedral : 4.071 17.232 1639 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1508 helix: 0.46 (0.30), residues: 274 sheet: -1.65 (0.25), residues: 355 loop : -2.02 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 49 HIS 0.005 0.001 HIS A 313 PHE 0.013 0.001 PHE C 86 TYR 0.019 0.001 TYR A 642 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8703 (tp30) REVERT: A 459 LEU cc_start: 0.9161 (mt) cc_final: 0.8908 (mt) REVERT: A 553 ASP cc_start: 0.8395 (t0) cc_final: 0.8088 (t0) REVERT: A 611 LEU cc_start: 0.9335 (mm) cc_final: 0.9114 (mm) REVERT: A 612 LYS cc_start: 0.8064 (pptt) cc_final: 0.7817 (pptt) REVERT: A 651 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9215 (tp30) REVERT: A 707 HIS cc_start: 0.8032 (m-70) cc_final: 0.7604 (m-70) REVERT: B 152 TRP cc_start: 0.8892 (m100) cc_final: 0.8666 (m100) REVERT: B 157 ASN cc_start: 0.9487 (m-40) cc_final: 0.9181 (p0) REVERT: B 218 TRP cc_start: 0.9344 (m-90) cc_final: 0.8273 (m-90) REVERT: B 220 ILE cc_start: 0.9320 (pt) cc_final: 0.9112 (pt) REVERT: B 225 LEU cc_start: 0.9459 (tt) cc_final: 0.8800 (pt) REVERT: B 226 VAL cc_start: 0.9770 (t) cc_final: 0.9535 (t) REVERT: B 252 MET cc_start: 0.9280 (mmm) cc_final: 0.8803 (mmm) REVERT: B 263 TRP cc_start: 0.7812 (m100) cc_final: 0.7148 (m100) REVERT: B 271 MET cc_start: 0.9274 (mmt) cc_final: 0.9055 (mmt) REVERT: B 291 SER cc_start: 0.9208 (t) cc_final: 0.8763 (p) REVERT: B 292 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8213 (mm-40) REVERT: B 294 ILE cc_start: 0.8769 (mm) cc_final: 0.8557 (mm) REVERT: B 314 TRP cc_start: 0.8048 (m100) cc_final: 0.7554 (m100) REVERT: B 315 LEU cc_start: 0.9580 (tp) cc_final: 0.9124 (tp) REVERT: B 331 TRP cc_start: 0.8728 (p-90) cc_final: 0.7319 (p-90) REVERT: B 362 ASP cc_start: 0.9125 (m-30) cc_final: 0.8909 (p0) REVERT: B 367 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8111 (mtt180) REVERT: B 376 MET cc_start: 0.8592 (ppp) cc_final: 0.8310 (ppp) REVERT: B 377 LEU cc_start: 0.8425 (tt) cc_final: 0.8099 (tp) REVERT: B 415 GLN cc_start: 0.7636 (tt0) cc_final: 0.7123 (tt0) REVERT: C 111 LEU cc_start: 0.9444 (mt) cc_final: 0.9176 (mp) REVERT: C 117 TYR cc_start: 0.6716 (p90) cc_final: 0.6449 (p90) REVERT: C 469 LEU cc_start: 0.9182 (mt) cc_final: 0.8904 (mt) REVERT: C 572 LEU cc_start: 0.9639 (mm) cc_final: 0.9407 (mm) REVERT: C 574 LEU cc_start: 0.8295 (tp) cc_final: 0.8073 (tp) REVERT: C 595 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8873 (mmmm) REVERT: C 615 LYS cc_start: 0.9080 (pttt) cc_final: 0.8747 (pttp) REVERT: C 618 ASN cc_start: 0.8446 (m110) cc_final: 0.8171 (m110) REVERT: C 629 ASP cc_start: 0.9113 (m-30) cc_final: 0.8722 (m-30) REVERT: C 684 MET cc_start: 0.8633 (mpp) cc_final: 0.8115 (mpp) REVERT: D 34 LEU cc_start: 0.9181 (mt) cc_final: 0.8654 (pp) REVERT: D 253 MET cc_start: 0.4572 (mpp) cc_final: 0.4192 (mpp) REVERT: D 322 GLN cc_start: 0.7473 (tp-100) cc_final: 0.5925 (mt0) REVERT: D 367 LEU cc_start: 0.9089 (tp) cc_final: 0.8713 (tt) REVERT: D 395 GLU cc_start: 0.9596 (pp20) cc_final: 0.9234 (pm20) REVERT: D 399 MET cc_start: 0.9469 (tmm) cc_final: 0.9112 (tmm) REVERT: D 403 GLN cc_start: 0.8407 (tt0) cc_final: 0.8149 (tm-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2143 time to fit residues: 70.0380 Evaluate side-chains 169 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 470 GLN A 636 ASN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS D 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12282 Z= 0.274 Angle : 0.664 9.406 16652 Z= 0.350 Chirality : 0.045 0.176 1833 Planarity : 0.004 0.052 2152 Dihedral : 4.917 20.584 1639 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % 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: -1.79 (0.21), residues: 1508 helix: 0.38 (0.31), residues: 286 sheet: -1.17 (0.26), residues: 364 loop : -1.78 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 325 HIS 0.007 0.002 HIS D 328 PHE 0.019 0.002 PHE A 308 TYR 0.023 0.002 TYR A 642 ARG 0.007 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8785 (tp30) REVERT: A 470 GLN cc_start: 0.9446 (mm110) cc_final: 0.9170 (mm110) REVERT: A 553 ASP cc_start: 0.8542 (t0) cc_final: 0.8306 (t0) REVERT: A 651 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9196 (tp30) REVERT: A 707 HIS cc_start: 0.8200 (m-70) cc_final: 0.7857 (m-70) REVERT: B 157 ASN cc_start: 0.9609 (m-40) cc_final: 0.9330 (p0) REVERT: B 195 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 218 TRP cc_start: 0.9149 (m-90) cc_final: 0.8173 (m-90) REVERT: B 252 MET cc_start: 0.9223 (mmm) cc_final: 0.8774 (mmm) REVERT: B 291 SER cc_start: 0.9083 (t) cc_final: 0.8653 (t) REVERT: B 314 TRP cc_start: 0.8079 (m100) cc_final: 0.7758 (m100) REVERT: B 315 LEU cc_start: 0.9589 (tp) cc_final: 0.9135 (tp) REVERT: B 331 TRP cc_start: 0.8782 (p-90) cc_final: 0.7341 (p-90) REVERT: B 376 MET cc_start: 0.9060 (ppp) cc_final: 0.8498 (ppp) REVERT: B 377 LEU cc_start: 0.8748 (tt) cc_final: 0.8378 (tp) REVERT: C 111 LEU cc_start: 0.9403 (mt) cc_final: 0.9169 (mp) REVERT: C 117 TYR cc_start: 0.6726 (p90) cc_final: 0.6216 (p90) REVERT: C 137 MET cc_start: 0.6963 (mmm) cc_final: 0.6759 (mpp) REVERT: C 569 ASP cc_start: 0.9090 (p0) cc_final: 0.8776 (p0) REVERT: C 570 THR cc_start: 0.8847 (p) cc_final: 0.8481 (p) REVERT: C 585 ASP cc_start: 0.7174 (t70) cc_final: 0.6698 (t0) REVERT: C 595 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8974 (mmmm) REVERT: C 622 MET cc_start: 0.9292 (mmp) cc_final: 0.9087 (mmm) REVERT: C 632 MET cc_start: 0.9523 (ppp) cc_final: 0.9285 (ppp) REVERT: D 20 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8705 (mt-10) REVERT: D 34 LEU cc_start: 0.9457 (mt) cc_final: 0.8999 (pp) REVERT: D 322 GLN cc_start: 0.7400 (tp-100) cc_final: 0.5718 (mt0) REVERT: D 367 LEU cc_start: 0.9163 (tp) cc_final: 0.8767 (tt) REVERT: D 399 MET cc_start: 0.9348 (tmm) cc_final: 0.8800 (tmm) REVERT: D 403 GLN cc_start: 0.8478 (tt0) cc_final: 0.8244 (tm-30) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1833 time to fit residues: 55.2728 Evaluate side-chains 142 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.0470 chunk 125 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 470 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 HIS C 618 ASN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12282 Z= 0.145 Angle : 0.537 7.134 16652 Z= 0.278 Chirality : 0.044 0.185 1833 Planarity : 0.003 0.037 2152 Dihedral : 4.316 17.826 1639 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.08 % Allowed : 1.51 % Favored : 98.41 % 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: -1.49 (0.21), residues: 1508 helix: 0.57 (0.31), residues: 287 sheet: -0.87 (0.27), residues: 361 loop : -1.63 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 49 HIS 0.005 0.001 HIS B 92 PHE 0.017 0.001 PHE A 725 TYR 0.022 0.001 TYR B 278 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8682 (tp30) REVERT: A 117 LEU cc_start: 0.9447 (mt) cc_final: 0.9247 (mm) REVERT: A 553 ASP cc_start: 0.8502 (t0) cc_final: 0.8186 (t0) REVERT: A 651 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9074 (tp30) REVERT: B 152 TRP cc_start: 0.9128 (m100) cc_final: 0.8588 (m100) REVERT: B 157 ASN cc_start: 0.9583 (m-40) cc_final: 0.9304 (p0) REVERT: B 195 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 218 TRP cc_start: 0.9273 (m-90) cc_final: 0.8501 (m-90) REVERT: B 252 MET cc_start: 0.9145 (mmm) cc_final: 0.8672 (tpp) REVERT: B 271 MET cc_start: 0.9289 (mmp) cc_final: 0.9081 (mmm) REVERT: B 314 TRP cc_start: 0.8061 (m100) cc_final: 0.7365 (m100) REVERT: B 315 LEU cc_start: 0.9583 (tp) cc_final: 0.9061 (tp) REVERT: B 331 TRP cc_start: 0.8743 (p-90) cc_final: 0.7280 (p-90) REVERT: B 340 ILE cc_start: 0.9439 (pt) cc_final: 0.8116 (pt) REVERT: B 376 MET cc_start: 0.9030 (ppp) cc_final: 0.8507 (ppp) REVERT: B 377 LEU cc_start: 0.8818 (tt) cc_final: 0.8381 (tp) REVERT: C 80 GLN cc_start: 0.4903 (tp-100) cc_final: 0.4505 (tp-100) REVERT: C 91 GLU cc_start: 0.8505 (tp30) cc_final: 0.8303 (tp30) REVERT: C 117 TYR cc_start: 0.6824 (p90) cc_final: 0.6142 (p90) REVERT: C 469 LEU cc_start: 0.9274 (mt) cc_final: 0.9048 (mt) REVERT: C 569 ASP cc_start: 0.8945 (p0) cc_final: 0.8547 (p0) REVERT: C 595 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8864 (mmmm) REVERT: C 612 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8158 (tp30) REVERT: C 618 ASN cc_start: 0.9110 (m-40) cc_final: 0.8846 (m-40) REVERT: C 622 MET cc_start: 0.9210 (mmp) cc_final: 0.8884 (mmp) REVERT: C 684 MET cc_start: 0.8825 (mpp) cc_final: 0.8320 (mpp) REVERT: D 20 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8705 (mt-10) REVERT: D 34 LEU cc_start: 0.9506 (mt) cc_final: 0.8945 (pp) REVERT: D 252 LEU cc_start: 0.9265 (mp) cc_final: 0.9056 (mp) REVERT: D 253 MET cc_start: 0.5124 (mpp) cc_final: 0.4630 (mpp) REVERT: D 276 VAL cc_start: 0.7124 (t) cc_final: 0.6912 (m) REVERT: D 367 LEU cc_start: 0.9208 (tp) cc_final: 0.8922 (tt) REVERT: D 395 GLU cc_start: 0.9606 (pp20) cc_final: 0.9304 (pm20) REVERT: D 399 MET cc_start: 0.9441 (tmm) cc_final: 0.8871 (tmm) REVERT: D 403 GLN cc_start: 0.8748 (tt0) cc_final: 0.8294 (mm-40) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2007 time to fit residues: 61.2750 Evaluate side-chains 151 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12282 Z= 0.144 Angle : 0.529 7.201 16652 Z= 0.275 Chirality : 0.043 0.158 1833 Planarity : 0.003 0.040 2152 Dihedral : 4.148 16.424 1639 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -1.31 (0.21), residues: 1508 helix: 0.71 (0.31), residues: 284 sheet: -0.79 (0.26), residues: 390 loop : -1.49 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 218 HIS 0.006 0.001 HIS B 92 PHE 0.012 0.001 PHE C 656 TYR 0.019 0.001 TYR A 659 ARG 0.005 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8738 (tp30) REVERT: A 553 ASP cc_start: 0.8479 (t0) cc_final: 0.8176 (t0) REVERT: A 651 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9052 (tp30) REVERT: A 717 ILE cc_start: 0.7117 (mm) cc_final: 0.6728 (mt) REVERT: B 115 THR cc_start: 0.9232 (p) cc_final: 0.8883 (t) REVERT: B 132 ILE cc_start: 0.9009 (mm) cc_final: 0.8698 (mp) REVERT: B 152 TRP cc_start: 0.9133 (m100) cc_final: 0.8562 (m100) REVERT: B 157 ASN cc_start: 0.9598 (m-40) cc_final: 0.9318 (p0) REVERT: B 195 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8380 (tm-30) REVERT: B 218 TRP cc_start: 0.9271 (m-90) cc_final: 0.8614 (m-90) REVERT: B 252 MET cc_start: 0.9161 (mmm) cc_final: 0.8730 (tpp) REVERT: B 271 MET cc_start: 0.9313 (mmp) cc_final: 0.9106 (mmm) REVERT: B 310 ASP cc_start: 0.7168 (m-30) cc_final: 0.6889 (m-30) REVERT: B 376 MET cc_start: 0.9053 (ppp) cc_final: 0.8451 (ppp) REVERT: B 377 LEU cc_start: 0.8851 (tt) cc_final: 0.8372 (tp) REVERT: B 415 GLN cc_start: 0.7021 (tt0) cc_final: 0.6622 (tt0) REVERT: C 80 GLN cc_start: 0.4605 (tp-100) cc_final: 0.4206 (tp-100) REVERT: C 111 LEU cc_start: 0.9448 (mt) cc_final: 0.9221 (mt) REVERT: C 117 TYR cc_start: 0.7186 (p90) cc_final: 0.6405 (p90) REVERT: C 469 LEU cc_start: 0.9266 (mt) cc_final: 0.9056 (mt) REVERT: C 569 ASP cc_start: 0.8964 (p0) cc_final: 0.8466 (p0) REVERT: C 570 THR cc_start: 0.8915 (p) cc_final: 0.8620 (p) REVERT: C 585 ASP cc_start: 0.6983 (t70) cc_final: 0.6693 (t0) REVERT: C 595 LYS cc_start: 0.9354 (mmmm) cc_final: 0.8972 (mmmm) REVERT: C 612 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8416 (tp30) REVERT: C 615 LYS cc_start: 0.9276 (pttt) cc_final: 0.8939 (ptmt) REVERT: C 622 MET cc_start: 0.9191 (mmp) cc_final: 0.8899 (mmp) REVERT: C 684 MET cc_start: 0.8621 (mpp) cc_final: 0.8124 (mpp) REVERT: D 20 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8701 (mt-10) REVERT: D 34 LEU cc_start: 0.9513 (mt) cc_final: 0.8931 (pp) REVERT: D 253 MET cc_start: 0.5525 (mpp) cc_final: 0.5056 (mpp) REVERT: D 322 GLN cc_start: 0.7603 (tp-100) cc_final: 0.5883 (mt0) REVERT: D 367 LEU cc_start: 0.9108 (tp) cc_final: 0.8853 (tt) REVERT: D 399 MET cc_start: 0.9441 (tmm) cc_final: 0.8822 (tmm) REVERT: D 403 GLN cc_start: 0.8783 (tt0) cc_final: 0.8332 (mm-40) REVERT: D 404 MET cc_start: 0.8240 (tmm) cc_final: 0.8032 (tmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1881 time to fit residues: 57.6331 Evaluate side-chains 151 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12282 Z= 0.221 Angle : 0.581 7.460 16652 Z= 0.306 Chirality : 0.044 0.169 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.497 19.713 1639 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -1.27 (0.21), residues: 1508 helix: 0.44 (0.30), residues: 285 sheet: -0.79 (0.26), residues: 376 loop : -1.32 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 452 HIS 0.005 0.001 HIS B 92 PHE 0.017 0.002 PHE C 86 TYR 0.019 0.002 TYR A 659 ARG 0.005 0.001 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5747 (pmm) cc_final: 0.5159 (pmm) REVERT: A 117 LEU cc_start: 0.9545 (mt) cc_final: 0.9323 (tp) REVERT: A 470 GLN cc_start: 0.9469 (mm110) cc_final: 0.9232 (mm110) REVERT: A 553 ASP cc_start: 0.8425 (t0) cc_final: 0.8121 (t0) REVERT: A 651 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9226 (tp30) REVERT: A 717 ILE cc_start: 0.6759 (mm) cc_final: 0.6422 (mt) REVERT: B 157 ASN cc_start: 0.9632 (m-40) cc_final: 0.9314 (p0) REVERT: B 218 TRP cc_start: 0.9233 (m-90) cc_final: 0.8561 (m-90) REVERT: B 252 MET cc_start: 0.9288 (mmm) cc_final: 0.8994 (mmm) REVERT: B 318 LEU cc_start: 0.9620 (mt) cc_final: 0.9386 (mt) REVERT: B 330 CYS cc_start: 0.9019 (t) cc_final: 0.8354 (t) REVERT: B 331 TRP cc_start: 0.8960 (p-90) cc_final: 0.7590 (p-90) REVERT: B 376 MET cc_start: 0.9146 (ppp) cc_final: 0.8608 (ppp) REVERT: B 377 LEU cc_start: 0.8939 (tt) cc_final: 0.8500 (tp) REVERT: B 415 GLN cc_start: 0.7313 (tt0) cc_final: 0.6868 (tt0) REVERT: C 80 GLN cc_start: 0.5056 (tp-100) cc_final: 0.4569 (tp-100) REVERT: C 111 LEU cc_start: 0.9419 (mt) cc_final: 0.9215 (mt) REVERT: C 117 TYR cc_start: 0.7315 (p90) cc_final: 0.6590 (p90) REVERT: C 137 MET cc_start: 0.6223 (mmp) cc_final: 0.5814 (mtp) REVERT: C 569 ASP cc_start: 0.9023 (p0) cc_final: 0.8529 (p0) REVERT: C 570 THR cc_start: 0.8926 (p) cc_final: 0.8632 (p) REVERT: C 595 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9044 (mmmm) REVERT: C 622 MET cc_start: 0.9249 (mmp) cc_final: 0.8923 (mmp) REVERT: C 684 MET cc_start: 0.8733 (mpp) cc_final: 0.8186 (mpp) REVERT: D 20 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8582 (mt-10) REVERT: D 34 LEU cc_start: 0.9556 (mt) cc_final: 0.8985 (pp) REVERT: D 253 MET cc_start: 0.5550 (mpp) cc_final: 0.5063 (mpp) REVERT: D 258 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8147 (mmp80) REVERT: D 322 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7495 (tm-30) REVERT: D 367 LEU cc_start: 0.9151 (tp) cc_final: 0.8884 (tt) REVERT: D 399 MET cc_start: 0.9379 (tmm) cc_final: 0.8793 (tmm) REVERT: D 403 GLN cc_start: 0.8802 (tt0) cc_final: 0.8436 (tm-30) REVERT: D 404 MET cc_start: 0.8303 (tmm) cc_final: 0.8040 (tmm) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1935 time to fit residues: 56.6129 Evaluate side-chains 142 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.7338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12282 Z= 0.151 Angle : 0.546 12.177 16652 Z= 0.283 Chirality : 0.043 0.159 1833 Planarity : 0.003 0.039 2152 Dihedral : 4.307 22.784 1639 Min Nonbonded Distance : 1.205 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1508 helix: 0.66 (0.31), residues: 286 sheet: -0.67 (0.26), residues: 394 loop : -1.21 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 388 HIS 0.013 0.001 HIS B 92 PHE 0.014 0.001 PHE C 90 TYR 0.017 0.001 TYR A 659 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6159 (pmm) cc_final: 0.5512 (pmm) REVERT: A 553 ASP cc_start: 0.8399 (t0) cc_final: 0.8183 (t0) REVERT: A 651 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9067 (tp30) REVERT: A 707 HIS cc_start: 0.8763 (m90) cc_final: 0.8284 (m90) REVERT: A 717 ILE cc_start: 0.6849 (mm) cc_final: 0.6459 (mt) REVERT: B 115 THR cc_start: 0.9264 (p) cc_final: 0.7710 (p) REVERT: B 152 TRP cc_start: 0.9101 (m100) cc_final: 0.8555 (m100) REVERT: B 157 ASN cc_start: 0.9602 (m-40) cc_final: 0.9341 (p0) REVERT: B 252 MET cc_start: 0.9110 (mmm) cc_final: 0.8842 (mmm) REVERT: B 271 MET cc_start: 0.9169 (mmp) cc_final: 0.8953 (mmt) REVERT: B 330 CYS cc_start: 0.9005 (t) cc_final: 0.8665 (t) REVERT: B 376 MET cc_start: 0.9195 (ppp) cc_final: 0.8670 (ppp) REVERT: B 415 GLN cc_start: 0.7310 (tt0) cc_final: 0.6867 (tt0) REVERT: C 80 GLN cc_start: 0.4438 (tp-100) cc_final: 0.3944 (tp-100) REVERT: C 111 LEU cc_start: 0.9455 (mt) cc_final: 0.9237 (mt) REVERT: C 117 TYR cc_start: 0.7325 (p90) cc_final: 0.6485 (p90) REVERT: C 137 MET cc_start: 0.6284 (mmp) cc_final: 0.5977 (mtp) REVERT: C 469 LEU cc_start: 0.9358 (mt) cc_final: 0.9057 (mt) REVERT: C 569 ASP cc_start: 0.9006 (p0) cc_final: 0.8514 (p0) REVERT: C 570 THR cc_start: 0.9008 (p) cc_final: 0.8709 (p) REVERT: C 595 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9010 (mmmm) REVERT: C 612 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8211 (tp30) REVERT: C 615 LYS cc_start: 0.9107 (pttt) cc_final: 0.8440 (ptmm) REVERT: C 621 VAL cc_start: 0.9374 (p) cc_final: 0.9044 (p) REVERT: C 622 MET cc_start: 0.9168 (mmp) cc_final: 0.8810 (mmp) REVERT: C 684 MET cc_start: 0.8682 (mpp) cc_final: 0.8290 (mpp) REVERT: D 20 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8644 (mt-10) REVERT: D 34 LEU cc_start: 0.9525 (mt) cc_final: 0.8911 (pp) REVERT: D 252 LEU cc_start: 0.9250 (mp) cc_final: 0.9002 (mp) REVERT: D 253 MET cc_start: 0.5221 (mpp) cc_final: 0.4701 (mpp) REVERT: D 367 LEU cc_start: 0.9040 (tp) cc_final: 0.8762 (tt) REVERT: D 399 MET cc_start: 0.9378 (tmm) cc_final: 0.8801 (tmm) REVERT: D 403 GLN cc_start: 0.8734 (tt0) cc_final: 0.8308 (tm-30) REVERT: D 404 MET cc_start: 0.8226 (tmm) cc_final: 0.7766 (tmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2154 time to fit residues: 62.1900 Evaluate side-chains 138 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.2980 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 292 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 272 HIS ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12282 Z= 0.144 Angle : 0.536 7.479 16652 Z= 0.277 Chirality : 0.043 0.181 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.181 21.676 1639 Min Nonbonded Distance : 1.210 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.89 (0.21), residues: 1508 helix: 0.73 (0.31), residues: 286 sheet: -0.58 (0.26), residues: 395 loop : -1.05 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 325 HIS 0.014 0.001 HIS B 92 PHE 0.016 0.001 PHE D 368 TYR 0.016 0.001 TYR A 659 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6301 (pmm) cc_final: 0.5860 (pmm) REVERT: A 553 ASP cc_start: 0.8345 (t0) cc_final: 0.8128 (t0) REVERT: A 651 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9119 (tp30) REVERT: A 702 MET cc_start: 0.8774 (ptm) cc_final: 0.8098 (tmm) REVERT: A 707 HIS cc_start: 0.8744 (m90) cc_final: 0.8248 (m90) REVERT: A 717 ILE cc_start: 0.6828 (mm) cc_final: 0.6414 (mt) REVERT: B 115 THR cc_start: 0.9258 (p) cc_final: 0.7624 (p) REVERT: B 152 TRP cc_start: 0.9103 (m100) cc_final: 0.8537 (m100) REVERT: B 157 ASN cc_start: 0.9587 (m-40) cc_final: 0.9351 (p0) REVERT: B 252 MET cc_start: 0.9020 (mmm) cc_final: 0.8796 (mmm) REVERT: B 271 MET cc_start: 0.9150 (mmp) cc_final: 0.8935 (mmt) REVERT: B 318 LEU cc_start: 0.9552 (mt) cc_final: 0.9341 (tt) REVERT: B 376 MET cc_start: 0.9197 (ppp) cc_final: 0.8661 (ppp) REVERT: C 80 GLN cc_start: 0.4496 (tp-100) cc_final: 0.4152 (tp-100) REVERT: C 111 LEU cc_start: 0.9442 (mt) cc_final: 0.9135 (mt) REVERT: C 117 TYR cc_start: 0.7295 (p90) cc_final: 0.6524 (p90) REVERT: C 137 MET cc_start: 0.6317 (mmp) cc_final: 0.6008 (mtp) REVERT: C 569 ASP cc_start: 0.9006 (p0) cc_final: 0.8505 (p0) REVERT: C 570 THR cc_start: 0.9065 (p) cc_final: 0.8782 (p) REVERT: C 612 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8459 (tp30) REVERT: C 621 VAL cc_start: 0.9371 (p) cc_final: 0.9024 (p) REVERT: C 622 MET cc_start: 0.9148 (mmp) cc_final: 0.8781 (mmp) REVERT: D 20 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8666 (mt-10) REVERT: D 34 LEU cc_start: 0.9483 (mt) cc_final: 0.8902 (pp) REVERT: D 252 LEU cc_start: 0.9246 (mp) cc_final: 0.9012 (mp) REVERT: D 253 MET cc_start: 0.5223 (mpp) cc_final: 0.4728 (mpp) REVERT: D 361 ASP cc_start: 0.7432 (m-30) cc_final: 0.7046 (m-30) REVERT: D 367 LEU cc_start: 0.9044 (tp) cc_final: 0.8746 (tt) REVERT: D 399 MET cc_start: 0.9189 (tmm) cc_final: 0.8747 (tmm) REVERT: D 403 GLN cc_start: 0.8660 (tt0) cc_final: 0.8253 (tp40) REVERT: D 404 MET cc_start: 0.8180 (tmm) cc_final: 0.7806 (tmm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2144 time to fit residues: 59.5791 Evaluate side-chains 134 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 151 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 128 optimal weight: 0.0050 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12282 Z= 0.143 Angle : 0.531 7.687 16652 Z= 0.275 Chirality : 0.043 0.176 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.186 21.508 1639 Min Nonbonded Distance : 1.217 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1508 helix: 0.77 (0.31), residues: 286 sheet: -0.43 (0.26), residues: 398 loop : -1.05 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.001 TRP D 325 HIS 0.011 0.001 HIS B 92 PHE 0.013 0.001 PHE D 368 TYR 0.016 0.001 TYR A 659 ARG 0.003 0.000 ARG B 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6557 (pmm) cc_final: 0.6117 (pmm) REVERT: A 297 LEU cc_start: 0.9275 (mm) cc_final: 0.8959 (mm) REVERT: A 553 ASP cc_start: 0.8382 (t0) cc_final: 0.8115 (t0) REVERT: A 651 GLU cc_start: 0.9517 (mm-30) cc_final: 0.9121 (tp30) REVERT: A 702 MET cc_start: 0.8748 (ptm) cc_final: 0.8091 (tmm) REVERT: A 707 HIS cc_start: 0.8780 (m90) cc_final: 0.8219 (m90) REVERT: A 717 ILE cc_start: 0.6810 (mm) cc_final: 0.6419 (mt) REVERT: B 115 THR cc_start: 0.9166 (p) cc_final: 0.7373 (p) REVERT: B 152 TRP cc_start: 0.9154 (m100) cc_final: 0.8243 (m100) REVERT: B 157 ASN cc_start: 0.9589 (m-40) cc_final: 0.9355 (p0) REVERT: B 209 VAL cc_start: 0.7861 (t) cc_final: 0.7345 (p) REVERT: B 252 MET cc_start: 0.9062 (mmm) cc_final: 0.8786 (mmm) REVERT: B 271 MET cc_start: 0.9157 (mmp) cc_final: 0.8910 (mmt) REVERT: B 294 ILE cc_start: 0.9081 (mm) cc_final: 0.8830 (tp) REVERT: B 330 CYS cc_start: 0.8945 (t) cc_final: 0.7623 (t) REVERT: B 376 MET cc_start: 0.9182 (ppp) cc_final: 0.8651 (ppp) REVERT: C 80 GLN cc_start: 0.4530 (tp-100) cc_final: 0.3964 (tp-100) REVERT: C 84 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8093 (tp30) REVERT: C 111 LEU cc_start: 0.9407 (mt) cc_final: 0.9130 (mt) REVERT: C 117 TYR cc_start: 0.7356 (p90) cc_final: 0.6513 (p90) REVERT: C 137 MET cc_start: 0.6404 (mmp) cc_final: 0.5958 (mtp) REVERT: C 569 ASP cc_start: 0.8976 (p0) cc_final: 0.8444 (p0) REVERT: C 570 THR cc_start: 0.8729 (p) cc_final: 0.8134 (p) REVERT: C 572 LEU cc_start: 0.9656 (mm) cc_final: 0.9400 (pp) REVERT: C 585 ASP cc_start: 0.6885 (t70) cc_final: 0.6610 (t0) REVERT: C 612 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8073 (tp30) REVERT: C 621 VAL cc_start: 0.9384 (p) cc_final: 0.9025 (p) REVERT: C 622 MET cc_start: 0.9153 (mmp) cc_final: 0.8790 (mmp) REVERT: D 20 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8675 (mt-10) REVERT: D 34 LEU cc_start: 0.9496 (mt) cc_final: 0.8902 (pp) REVERT: D 252 LEU cc_start: 0.9227 (mp) cc_final: 0.9017 (mp) REVERT: D 253 MET cc_start: 0.5434 (mpp) cc_final: 0.5033 (mpp) REVERT: D 361 ASP cc_start: 0.7519 (m-30) cc_final: 0.7130 (m-30) REVERT: D 367 LEU cc_start: 0.9027 (tp) cc_final: 0.8774 (tt) REVERT: D 399 MET cc_start: 0.9203 (tmm) cc_final: 0.8768 (tmm) REVERT: D 403 GLN cc_start: 0.8804 (tt0) cc_final: 0.8496 (tm-30) REVERT: D 404 MET cc_start: 0.8208 (tmm) cc_final: 0.8006 (tmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2007 time to fit residues: 56.9583 Evaluate side-chains 136 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 292 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.080390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059897 restraints weight = 58869.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.061571 restraints weight = 38896.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062777 restraints weight = 28768.466| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12282 Z= 0.145 Angle : 0.538 7.601 16652 Z= 0.278 Chirality : 0.043 0.196 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.143 20.736 1639 Min Nonbonded Distance : 1.215 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -0.82 (0.21), residues: 1508 helix: 0.72 (0.31), residues: 280 sheet: -0.44 (0.26), residues: 390 loop : -1.02 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 325 HIS 0.011 0.001 HIS B 92 PHE 0.016 0.001 PHE B 198 TYR 0.016 0.001 TYR A 659 ARG 0.002 0.000 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.73 seconds wall clock time: 47 minutes 31.42 seconds (2851.42 seconds total)