Starting phenix.real_space_refine on Mon Mar 18 23:45:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/03_2024/8gvw_34300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/03_2024/8gvw_34300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/03_2024/8gvw_34300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/03_2024/8gvw_34300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/03_2024/8gvw_34300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/03_2024/8gvw_34300.pdb" } resolution = 3.59 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= 0.079 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14760 2.51 5 N 3604 2.21 5 O 4000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 439": "OD1" <-> "OD2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 559": "OE1" <-> "OE2" Residue "C GLU 653": "OE1" <-> "OE2" Residue "C TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D GLU 559": "OE1" <-> "OE2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 756": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22496 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "B" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "C" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "D" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5467 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 646} Chain breaks: 4 Chain: "A" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 55.311 14.352 74.606 1.00132.73 S ATOM 1162 SG CYS A 178 52.994 12.329 76.873 1.00138.45 S ATOM 1184 SG CYS A 181 52.833 16.060 76.972 1.00127.14 S ATOM 6615 SG CYS B 176 14.361 61.965 74.612 1.00132.17 S ATOM 6629 SG CYS B 178 12.338 64.281 76.880 1.00139.50 S ATOM 6651 SG CYS B 181 16.070 64.443 76.978 1.00128.47 S ATOM 12082 SG CYS C 176 61.976 102.914 74.620 1.00133.10 S ATOM 12096 SG CYS C 178 64.292 104.937 76.888 1.00139.63 S ATOM 12118 SG CYS C 181 64.454 101.205 76.986 1.00128.34 S ATOM 17549 SG CYS D 176 102.925 55.300 74.613 1.00132.40 S ATOM 17563 SG CYS D 178 104.948 52.983 76.880 1.00138.94 S ATOM 17585 SG CYS D 181 101.216 52.821 76.978 1.00127.06 S Time building chain proxies: 11.89, per 1000 atoms: 0.53 Number of scatterers: 22496 At special positions: 0 Unit cell: (118.374, 118.374, 136.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 4000 8.00 N 3604 7.00 C 14760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " Number of angles added : 12 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.852A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.865A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.829A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.668A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 707 through 733 Processing helix chain 'A' and resid 739 through 761 removed outlier: 3.892A pdb=" N PHE A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.851A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.866A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.828A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.669A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 Processing helix chain 'B' and resid 707 through 733 Processing helix chain 'B' and resid 739 through 761 removed outlier: 3.892A pdb=" N PHE B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.852A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.866A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.829A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 499 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.669A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 Processing helix chain 'C' and resid 707 through 733 Processing helix chain 'C' and resid 739 through 761 removed outlier: 3.891A pdb=" N PHE C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.666A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 4.033A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.852A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.922A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.865A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.828A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 499 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.367A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.669A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 633 removed outlier: 3.783A pdb=" N GLN D 629 " --> pdb=" O ASN D 625 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 Processing helix chain 'D' and resid 707 through 733 Processing helix chain 'D' and resid 739 through 761 removed outlier: 3.892A pdb=" N PHE D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3577 1.32 - 1.44: 6127 1.44 - 1.57: 13088 1.57 - 1.69: 24 1.69 - 1.81: 188 Bond restraints: 23004 Sorted by residual: bond pdb=" O12 POV A 802 " pdb=" P POV A 802 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" O12 POV D 802 " pdb=" P POV D 802 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" CB PRO C 398 " pdb=" CG PRO C 398 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.56e+00 bond pdb=" O12 POV B 802 " pdb=" P POV B 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 22999 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.10: 396 105.10 - 112.47: 11578 112.47 - 119.83: 8492 119.83 - 127.19: 10330 127.19 - 134.56: 300 Bond angle restraints: 31096 Sorted by residual: angle pdb=" CA PRO C 398 " pdb=" N PRO C 398 " pdb=" CD PRO C 398 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 angle pdb=" CA PRO A 398 " pdb=" N PRO A 398 " pdb=" CD PRO A 398 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" CD PRO B 398 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO D 398 " pdb=" N PRO D 398 " pdb=" CD PRO D 398 " ideal model delta sigma weight residual 112.00 105.78 6.22 1.40e+00 5.10e-01 1.97e+01 angle pdb=" CA PHE D 753 " pdb=" CB PHE D 753 " pdb=" CG PHE D 753 " ideal model delta sigma weight residual 113.80 117.54 -3.74 1.00e+00 1.00e+00 1.40e+01 ... (remaining 31091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 13720 34.94 - 69.87: 268 69.87 - 104.81: 28 104.81 - 139.74: 20 139.74 - 174.68: 4 Dihedral angle restraints: 14040 sinusoidal: 6096 harmonic: 7944 Sorted by residual: dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -55.57 174.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 807 " pdb=" C27 YZY A 807 " pdb=" C28 YZY A 807 " pdb=" C29 YZY A 807 " ideal model delta sinusoidal sigma weight residual 119.11 -55.56 174.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -55.53 174.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 14037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2724 0.052 - 0.105: 608 0.105 - 0.157: 120 0.157 - 0.209: 20 0.209 - 0.262: 4 Chirality restraints: 3476 Sorted by residual: chirality pdb=" CB VAL C 590 " pdb=" CA VAL C 590 " pdb=" CG1 VAL C 590 " pdb=" CG2 VAL C 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL D 590 " pdb=" CA VAL D 590 " pdb=" CG1 VAL D 590 " pdb=" CG2 VAL D 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL A 590 " pdb=" CA VAL A 590 " pdb=" CG1 VAL A 590 " pdb=" CG2 VAL A 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3473 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 397 " 0.049 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO B 398 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 397 " 0.049 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO A 398 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 397 " 0.049 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO C 398 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 398 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 398 " 0.039 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3938 2.77 - 3.30: 21644 3.30 - 3.83: 36931 3.83 - 4.37: 42327 4.37 - 4.90: 74193 Nonbonded interactions: 179033 Sorted by model distance: nonbonded pdb=" OH TYR C 374 " pdb=" O SER C 489 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR A 374 " pdb=" O SER A 489 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR D 374 " pdb=" O SER D 489 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR B 374 " pdb=" O SER B 489 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP C 215 " pdb=" OH TYR C 713 " model vdw 2.288 2.440 ... (remaining 179028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 761 or resid 801 through 805)) selection = (chain 'B' and (resid 17 through 761 or resid 801 through 805)) selection = (chain 'C' and (resid 17 through 761 or resid 801 through 805)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.720 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 58.080 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.140 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.006 0.128 23004 Z= 0.361 Angle : 0.894 9.558 31096 Z= 0.464 Chirality : 0.047 0.262 3476 Planarity : 0.007 0.081 3828 Dihedral : 15.334 174.677 8860 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.17 % Allowed : 0.67 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.01 (0.15), residues: 2644 helix: 0.35 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.71 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 410 HIS 0.003 0.001 HIS B 735 PHE 0.038 0.002 PHE B 753 TYR 0.032 0.002 TYR C 724 ARG 0.007 0.001 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 515 time to evaluate : 2.518 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8396 (pttm) cc_final: 0.7659 (pttm) REVERT: A 48 VAL cc_start: 0.9046 (t) cc_final: 0.8833 (p) REVERT: A 479 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 598 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8146 (mm-30) REVERT: A 628 TYR cc_start: 0.8945 (t80) cc_final: 0.8675 (t80) REVERT: A 728 MET cc_start: 0.7780 (ttp) cc_final: 0.7564 (ttp) REVERT: B 42 LYS cc_start: 0.8404 (pttm) cc_final: 0.7680 (pttm) REVERT: B 48 VAL cc_start: 0.9061 (t) cc_final: 0.8831 (p) REVERT: B 598 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8146 (mm-30) REVERT: B 628 TYR cc_start: 0.8936 (t80) cc_final: 0.8667 (t80) REVERT: C 42 LYS cc_start: 0.8408 (pttm) cc_final: 0.7639 (pttm) REVERT: C 48 VAL cc_start: 0.9086 (t) cc_final: 0.8873 (p) REVERT: C 598 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 628 TYR cc_start: 0.8943 (t80) cc_final: 0.8627 (t80) REVERT: C 728 MET cc_start: 0.7835 (ttp) cc_final: 0.7612 (ttp) REVERT: D 42 LYS cc_start: 0.8408 (pttm) cc_final: 0.7649 (pttm) REVERT: D 541 TYR cc_start: 0.7959 (m-10) cc_final: 0.7759 (m-10) REVERT: D 728 MET cc_start: 0.7812 (ttp) cc_final: 0.7597 (ttp) outliers start: 4 outliers final: 0 residues processed: 515 average time/residue: 0.2988 time to fit residues: 248.1108 Evaluate side-chains 384 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 1.9990 chunk 203 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 0.0670 chunk 210 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23004 Z= 0.201 Angle : 0.545 6.556 31096 Z= 0.280 Chirality : 0.038 0.161 3476 Planarity : 0.004 0.043 3828 Dihedral : 12.441 116.741 3576 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.67 % Allowed : 10.02 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.29 (0.16), residues: 2644 helix: 1.36 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 315 HIS 0.002 0.001 HIS A 735 PHE 0.013 0.001 PHE C 540 TYR 0.015 0.001 TYR C 118 ARG 0.004 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 417 time to evaluate : 2.347 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: A 114 LEU cc_start: 0.8925 (mm) cc_final: 0.8550 (mm) REVERT: A 337 ILE cc_start: 0.8994 (mm) cc_final: 0.8773 (mt) REVERT: A 340 LEU cc_start: 0.9238 (mt) cc_final: 0.9034 (mp) REVERT: A 479 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 65 CYS cc_start: 0.8261 (p) cc_final: 0.8042 (p) REVERT: B 337 ILE cc_start: 0.9000 (mm) cc_final: 0.8781 (mt) REVERT: B 541 TYR cc_start: 0.7924 (m-10) cc_final: 0.7552 (m-10) REVERT: C 65 CYS cc_start: 0.8269 (p) cc_final: 0.8047 (p) REVERT: C 114 LEU cc_start: 0.8944 (mm) cc_final: 0.8584 (mm) REVERT: C 337 ILE cc_start: 0.8992 (mm) cc_final: 0.8761 (mt) REVERT: C 340 LEU cc_start: 0.9244 (mt) cc_final: 0.9029 (mp) REVERT: C 427 PHE cc_start: 0.7930 (t80) cc_final: 0.7576 (t80) REVERT: C 541 TYR cc_start: 0.7928 (m-10) cc_final: 0.7552 (m-10) REVERT: D 65 CYS cc_start: 0.8390 (p) cc_final: 0.8049 (p) REVERT: D 114 LEU cc_start: 0.8950 (mm) cc_final: 0.8587 (mm) REVERT: D 337 ILE cc_start: 0.8971 (mm) cc_final: 0.8745 (mt) REVERT: D 340 LEU cc_start: 0.9233 (mt) cc_final: 0.9021 (mp) REVERT: D 541 TYR cc_start: 0.7975 (m-10) cc_final: 0.7641 (m-10) outliers start: 16 outliers final: 16 residues processed: 426 average time/residue: 0.2874 time to fit residues: 201.1502 Evaluate side-chains 377 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 361 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 165 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 195 optimal weight: 0.0270 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23004 Z= 0.194 Angle : 0.518 6.744 31096 Z= 0.266 Chirality : 0.038 0.185 3476 Planarity : 0.004 0.042 3828 Dihedral : 11.350 114.901 3576 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.25 % Allowed : 12.81 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.82 (0.16), residues: 2644 helix: 1.77 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.42 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 315 HIS 0.003 0.000 HIS B 151 PHE 0.012 0.001 PHE B 540 TYR 0.018 0.001 TYR A 118 ARG 0.002 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 389 time to evaluate : 2.598 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.8976 (mmm) cc_final: 0.8684 (mmm) REVERT: A 114 LEU cc_start: 0.8979 (mm) cc_final: 0.8654 (mm) REVERT: A 337 ILE cc_start: 0.8964 (mm) cc_final: 0.8744 (mt) REVERT: A 479 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 539 TYR cc_start: 0.9199 (m-80) cc_final: 0.8838 (m-80) REVERT: A 541 TYR cc_start: 0.8037 (m-10) cc_final: 0.7812 (m-10) REVERT: B 33 GLU cc_start: 0.8236 (tt0) cc_final: 0.7990 (tp30) REVERT: B 66 MET cc_start: 0.8893 (mmm) cc_final: 0.8568 (mmm) REVERT: B 114 LEU cc_start: 0.8994 (mm) cc_final: 0.8666 (mm) REVERT: B 539 TYR cc_start: 0.9200 (m-80) cc_final: 0.8852 (m-80) REVERT: B 541 TYR cc_start: 0.8038 (m-10) cc_final: 0.7816 (m-10) REVERT: B 741 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8041 (mp0) REVERT: B 742 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.6600 (t0) REVERT: B 744 LYS cc_start: 0.7160 (mtmm) cc_final: 0.6928 (mtmm) REVERT: C 33 GLU cc_start: 0.8218 (tt0) cc_final: 0.7992 (tp30) REVERT: C 66 MET cc_start: 0.8891 (mmm) cc_final: 0.8568 (mmm) REVERT: C 114 LEU cc_start: 0.8994 (mm) cc_final: 0.8670 (mm) REVERT: C 337 ILE cc_start: 0.8941 (mm) cc_final: 0.8699 (mt) REVERT: C 539 TYR cc_start: 0.9199 (m-80) cc_final: 0.8850 (m-80) REVERT: C 541 TYR cc_start: 0.8041 (m-10) cc_final: 0.7817 (m-10) REVERT: D 65 CYS cc_start: 0.8109 (p) cc_final: 0.7610 (p) REVERT: D 66 MET cc_start: 0.8905 (mmm) cc_final: 0.8402 (mmm) REVERT: D 114 LEU cc_start: 0.8995 (mm) cc_final: 0.8675 (mm) REVERT: D 337 ILE cc_start: 0.8935 (mm) cc_final: 0.8691 (mp) REVERT: D 539 TYR cc_start: 0.9187 (m-80) cc_final: 0.8812 (m-80) REVERT: D 541 TYR cc_start: 0.7940 (m-10) cc_final: 0.7633 (m-10) outliers start: 30 outliers final: 23 residues processed: 411 average time/residue: 0.2992 time to fit residues: 198.8207 Evaluate side-chains 374 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 350 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 21 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23004 Z= 0.261 Angle : 0.548 9.334 31096 Z= 0.278 Chirality : 0.039 0.284 3476 Planarity : 0.004 0.044 3828 Dihedral : 11.200 123.735 3576 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.13 % Allowed : 13.90 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.01 (0.16), residues: 2644 helix: 1.93 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.40 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 315 HIS 0.004 0.001 HIS D 151 PHE 0.014 0.002 PHE C 341 TYR 0.016 0.001 TYR C 524 ARG 0.004 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 371 time to evaluate : 2.255 Fit side-chains REVERT: A 337 ILE cc_start: 0.9010 (mm) cc_final: 0.8765 (mp) REVERT: A 479 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 541 TYR cc_start: 0.8131 (m-10) cc_final: 0.7575 (m-10) REVERT: A 742 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.6619 (t0) REVERT: B 541 TYR cc_start: 0.8129 (m-10) cc_final: 0.7567 (m-10) REVERT: C 337 ILE cc_start: 0.9008 (mm) cc_final: 0.8769 (mp) REVERT: C 541 TYR cc_start: 0.8124 (m-10) cc_final: 0.7560 (m-10) REVERT: D 21 GLN cc_start: 0.6689 (mm110) cc_final: 0.6474 (mp10) REVERT: D 539 TYR cc_start: 0.9194 (m-80) cc_final: 0.8873 (m-80) REVERT: D 541 TYR cc_start: 0.8039 (m-10) cc_final: 0.7803 (m-10) REVERT: D 742 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.6591 (t0) outliers start: 51 outliers final: 36 residues processed: 407 average time/residue: 0.2937 time to fit residues: 193.9183 Evaluate side-chains 389 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 351 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 91 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 23004 Z= 0.425 Angle : 0.687 9.542 31096 Z= 0.344 Chirality : 0.044 0.179 3476 Planarity : 0.004 0.045 3828 Dihedral : 11.588 139.233 3576 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.55 % Allowed : 15.98 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.80 (0.16), residues: 2644 helix: 1.76 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.42 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 315 HIS 0.007 0.001 HIS D 151 PHE 0.017 0.003 PHE B 565 TYR 0.021 0.002 TYR C 524 ARG 0.004 0.001 ARG D 754 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 427 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.6887 (mm110) cc_final: 0.6629 (mp10) REVERT: A 66 MET cc_start: 0.8956 (mmm) cc_final: 0.8728 (mmm) REVERT: A 157 ILE cc_start: 0.8767 (mm) cc_final: 0.8548 (mm) REVERT: A 471 MET cc_start: 0.8594 (tmm) cc_final: 0.8390 (tmm) REVERT: A 628 TYR cc_start: 0.9063 (t80) cc_final: 0.8807 (t80) REVERT: B 21 GLN cc_start: 0.6842 (mm110) cc_final: 0.6612 (mp10) REVERT: B 471 MET cc_start: 0.8592 (tmm) cc_final: 0.8389 (tmm) REVERT: C 21 GLN cc_start: 0.6884 (mm110) cc_final: 0.6655 (mp10) REVERT: C 75 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (mm) REVERT: C 157 ILE cc_start: 0.8775 (mm) cc_final: 0.8571 (mm) REVERT: C 471 MET cc_start: 0.8582 (tmm) cc_final: 0.8378 (tmm) REVERT: C 628 TYR cc_start: 0.9058 (t80) cc_final: 0.8798 (t80) REVERT: D 157 ILE cc_start: 0.8758 (mm) cc_final: 0.8541 (mm) REVERT: D 628 TYR cc_start: 0.9058 (t80) cc_final: 0.8795 (t80) REVERT: D 744 LYS cc_start: 0.7117 (mtmm) cc_final: 0.6888 (mttp) outliers start: 61 outliers final: 39 residues processed: 466 average time/residue: 0.2984 time to fit residues: 224.1557 Evaluate side-chains 419 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 379 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 609 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 609 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 609 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN D 91 ASN D 609 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23004 Z= 0.227 Angle : 0.557 8.841 31096 Z= 0.279 Chirality : 0.039 0.182 3476 Planarity : 0.004 0.046 3828 Dihedral : 11.276 131.843 3576 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 17.65 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.18 (0.16), residues: 2644 helix: 2.02 (0.12), residues: 1976 sheet: None (None), residues: 0 loop : -0.26 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 315 HIS 0.003 0.001 HIS A 151 PHE 0.014 0.001 PHE B 341 TYR 0.026 0.001 TYR C 457 ARG 0.004 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 401 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.6951 (mm110) cc_final: 0.6718 (mp10) REVERT: A 90 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8569 (mm) REVERT: A 157 ILE cc_start: 0.8703 (mm) cc_final: 0.8496 (mm) REVERT: A 628 TYR cc_start: 0.9009 (t80) cc_final: 0.8735 (t80) REVERT: B 21 GLN cc_start: 0.6899 (mm110) cc_final: 0.6676 (mp10) REVERT: B 90 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8558 (mm) REVERT: B 742 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.6605 (t0) REVERT: B 744 LYS cc_start: 0.7522 (mtmm) cc_final: 0.7289 (mttp) REVERT: C 21 GLN cc_start: 0.6909 (mm110) cc_final: 0.6668 (mp10) REVERT: C 90 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 628 TYR cc_start: 0.8999 (t80) cc_final: 0.8725 (t80) REVERT: D 90 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8556 (mm) REVERT: D 157 ILE cc_start: 0.8696 (mm) cc_final: 0.8494 (mm) REVERT: D 628 TYR cc_start: 0.8995 (t80) cc_final: 0.8726 (t80) outliers start: 54 outliers final: 28 residues processed: 435 average time/residue: 0.3097 time to fit residues: 215.0383 Evaluate side-chains 399 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 366 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 0.0050 chunk 189 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 144 optimal weight: 0.0870 chunk 258 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C 711 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN D 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23004 Z= 0.153 Angle : 0.519 9.805 31096 Z= 0.262 Chirality : 0.038 0.229 3476 Planarity : 0.004 0.047 3828 Dihedral : 10.787 122.823 3576 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.21 % Allowed : 19.20 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.43 (0.17), residues: 2644 helix: 2.20 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.13 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 315 HIS 0.002 0.001 HIS C 326 PHE 0.014 0.001 PHE C 139 TYR 0.035 0.002 TYR D 541 ARG 0.004 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 405 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7011 (mm110) cc_final: 0.6738 (mp10) REVERT: A 90 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8493 (mm) REVERT: A 157 ILE cc_start: 0.8746 (mm) cc_final: 0.8522 (mm) REVERT: A 479 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: A 742 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.6526 (t0) REVERT: B 21 GLN cc_start: 0.6898 (mm110) cc_final: 0.6652 (mp10) REVERT: B 90 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8491 (mm) REVERT: B 479 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 541 TYR cc_start: 0.8155 (m-10) cc_final: 0.7607 (m-10) REVERT: B 741 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 742 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.6612 (t0) REVERT: B 744 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7225 (mttp) REVERT: C 21 GLN cc_start: 0.6979 (mm110) cc_final: 0.6732 (mp10) REVERT: C 90 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8529 (mm) REVERT: C 479 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7115 (mm-30) REVERT: D 90 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8519 (mm) REVERT: D 157 ILE cc_start: 0.8720 (mm) cc_final: 0.8490 (mm) REVERT: D 479 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7199 (mm-30) REVERT: D 541 TYR cc_start: 0.8635 (m-10) cc_final: 0.7729 (m-80) REVERT: D 742 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.6424 (t0) outliers start: 29 outliers final: 13 residues processed: 419 average time/residue: 0.3352 time to fit residues: 222.6976 Evaluate side-chains 378 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 357 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 154 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 164 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23004 Z= 0.192 Angle : 0.540 8.351 31096 Z= 0.273 Chirality : 0.039 0.177 3476 Planarity : 0.004 0.047 3828 Dihedral : 10.568 122.509 3576 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.88 % Allowed : 17.82 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.48 (0.17), residues: 2644 helix: 2.24 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.12 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.003 0.001 HIS A 192 PHE 0.014 0.001 PHE C 540 TYR 0.034 0.002 TYR D 541 ARG 0.003 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 379 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7067 (mm110) cc_final: 0.6784 (mp10) REVERT: A 90 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8560 (mm) REVERT: A 236 GLU cc_start: 0.7631 (pm20) cc_final: 0.7425 (mp0) REVERT: A 742 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.6503 (t0) REVERT: B 21 GLN cc_start: 0.6933 (mm110) cc_final: 0.6689 (mp10) REVERT: B 90 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8540 (mm) REVERT: B 236 GLU cc_start: 0.7671 (pm20) cc_final: 0.7450 (mp0) REVERT: B 741 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 742 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.6578 (t0) REVERT: C 21 GLN cc_start: 0.6950 (mm110) cc_final: 0.6700 (mp10) REVERT: C 90 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 422 MET cc_start: 0.8793 (tpp) cc_final: 0.8476 (tpt) REVERT: C 479 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7273 (mm-30) REVERT: D 90 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8546 (mm) REVERT: D 742 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.6458 (t0) outliers start: 45 outliers final: 24 residues processed: 404 average time/residue: 0.3211 time to fit residues: 204.2295 Evaluate side-chains 385 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 354 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 189 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23004 Z= 0.241 Angle : 0.579 9.434 31096 Z= 0.294 Chirality : 0.041 0.238 3476 Planarity : 0.004 0.047 3828 Dihedral : 10.526 123.112 3576 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.38 % Allowed : 18.70 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.41 (0.17), residues: 2644 helix: 2.20 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.18 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 315 HIS 0.003 0.001 HIS B 192 PHE 0.016 0.002 PHE D 540 TYR 0.037 0.002 TYR D 541 ARG 0.003 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 372 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8565 (mm) REVERT: A 236 GLU cc_start: 0.7650 (pm20) cc_final: 0.7423 (mp0) REVERT: A 319 PHE cc_start: 0.7895 (m-80) cc_final: 0.7520 (m-80) REVERT: A 541 TYR cc_start: 0.8150 (m-10) cc_final: 0.7887 (m-10) REVERT: A 595 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7411 (tt0) REVERT: A 742 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.6518 (t0) REVERT: B 90 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8549 (mm) REVERT: B 236 GLU cc_start: 0.7659 (pm20) cc_final: 0.7428 (mp0) REVERT: B 319 PHE cc_start: 0.7919 (m-80) cc_final: 0.7553 (m-80) REVERT: B 595 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7433 (tt0) REVERT: B 741 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 742 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.6645 (t0) REVERT: C 66 MET cc_start: 0.9146 (tpp) cc_final: 0.8946 (tpp) REVERT: C 90 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8565 (mm) REVERT: C 319 PHE cc_start: 0.7895 (m-80) cc_final: 0.7541 (m-80) REVERT: C 541 TYR cc_start: 0.8104 (m-10) cc_final: 0.7880 (m-10) REVERT: D 90 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8572 (mm) REVERT: D 319 PHE cc_start: 0.7913 (m-80) cc_final: 0.7535 (m-80) REVERT: D 742 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.6431 (t0) outliers start: 33 outliers final: 25 residues processed: 387 average time/residue: 0.3195 time to fit residues: 194.3853 Evaluate side-chains 383 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 351 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 266 optimal weight: 0.9990 chunk 245 optimal weight: 0.0870 chunk 212 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 168 optimal weight: 0.0000 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23004 Z= 0.173 Angle : 0.553 9.607 31096 Z= 0.281 Chirality : 0.039 0.192 3476 Planarity : 0.004 0.048 3828 Dihedral : 10.267 118.243 3576 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.25 % Allowed : 19.37 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.49 (0.17), residues: 2644 helix: 2.25 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.11 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.002 0.000 HIS C 151 PHE 0.015 0.001 PHE B 540 TYR 0.038 0.002 TYR D 541 ARG 0.007 0.000 ARG D 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 363 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 236 GLU cc_start: 0.7616 (pm20) cc_final: 0.7410 (mp0) REVERT: A 319 PHE cc_start: 0.7899 (m-80) cc_final: 0.7516 (m-80) REVERT: A 541 TYR cc_start: 0.8071 (m-10) cc_final: 0.7853 (m-10) REVERT: A 595 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7488 (tt0) REVERT: A 742 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.6448 (t0) REVERT: B 21 GLN cc_start: 0.7369 (mm110) cc_final: 0.7139 (mm110) REVERT: B 90 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8525 (mm) REVERT: B 236 GLU cc_start: 0.7619 (pm20) cc_final: 0.7415 (mp0) REVERT: B 512 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7519 (mtp85) REVERT: B 595 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7509 (tt0) REVERT: B 742 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.6543 (t0) REVERT: C 21 GLN cc_start: 0.7361 (mm110) cc_final: 0.7139 (mm110) REVERT: C 90 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8536 (mm) REVERT: C 319 PHE cc_start: 0.7872 (m-80) cc_final: 0.7524 (m-80) REVERT: C 446 TYR cc_start: 0.7434 (m-80) cc_final: 0.7066 (m-80) REVERT: C 541 TYR cc_start: 0.8075 (m-10) cc_final: 0.7853 (m-10) REVERT: D 90 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8575 (mm) REVERT: D 446 TYR cc_start: 0.7413 (m-80) cc_final: 0.7089 (m-80) REVERT: D 742 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.6336 (t0) outliers start: 30 outliers final: 18 residues processed: 377 average time/residue: 0.3283 time to fit residues: 197.0357 Evaluate side-chains 371 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 346 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 742 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 218 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 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 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122081 restraints weight = 29543.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119914 restraints weight = 20153.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121923 restraints weight = 18776.249| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23004 Z= 0.219 Angle : 0.571 9.610 31096 Z= 0.288 Chirality : 0.039 0.176 3476 Planarity : 0.004 0.055 3828 Dihedral : 10.209 119.042 3576 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.42 % Allowed : 19.62 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.45 (0.17), residues: 2644 helix: 2.21 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.08 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 315 HIS 0.002 0.001 HIS C 151 PHE 0.014 0.001 PHE C 540 TYR 0.035 0.002 TYR D 541 ARG 0.004 0.000 ARG B 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.67 seconds wall clock time: 81 minutes 39.67 seconds (4899.67 seconds total)