Starting phenix.real_space_refine on Sat Nov 18 09:20:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/11_2023/8gvw_34300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/11_2023/8gvw_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_34300/11_2023/8gvw_34300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/11_2023/8gvw_34300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/11_2023/8gvw_34300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvw_34300/11_2023/8gvw_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-1.21rc1-5144/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: 11.06, per 1000 atoms: 0.49 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: 9.86 Conformation dependent library (CDL) restraints added in 3.9 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: 1.94 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: 7.21 Time building geometry restraints manager: 10.44 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: 13432 34.94 - 69.87: 252 69.87 - 104.81: 28 104.81 - 139.74: 20 139.74 - 174.68: 4 Dihedral angle restraints: 13736 sinusoidal: 5792 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 13733 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.820 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 62.850 Find NCS groups from input model: 1.810 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.180 ------------------------------------------------------------------------------- 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 : 15.355 174.677 8556 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 *********************** 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 : 2.519 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 515 average time/residue: 0.3035 time to fit residues: 252.9678 Evaluate side-chains 378 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6720 ------------------------------------------------------------------------------- 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: 1.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 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: 1.1722 ------------------------------------------------------------------------------- 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** B 709 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 GLN D 21 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23004 Z= 0.298 Angle : 0.602 6.601 31096 Z= 0.310 Chirality : 0.040 0.166 3476 Planarity : 0.004 0.043 3828 Dihedral : 12.230 116.835 3272 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.83 % Allowed : 10.43 % Favored : 88.73 % 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: 1.24 (0.16), residues: 2644 helix: 1.32 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.51 (0.23), residues: 680 *********************** 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 454 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 434 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 20 residues processed: 442 average time/residue: 0.3100 time to fit residues: 220.2491 Evaluate side-chains 395 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 375 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2054 time to fit residues: 11.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 0.0980 chunk 263 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 195 optimal weight: 0.4980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 21 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23004 Z= 0.159 Angle : 0.520 6.577 31096 Z= 0.264 Chirality : 0.038 0.161 3476 Planarity : 0.004 0.043 3828 Dihedral : 11.254 112.430 3272 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.79 % Allowed : 13.44 % Favored : 85.77 % 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: 1.78 (0.16), residues: 2644 helix: 1.75 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.46 (0.22), residues: 672 *********************** 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 400 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 381 time to evaluate : 2.641 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 396 average time/residue: 0.3172 time to fit residues: 201.5611 Evaluate side-chains 359 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 343 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1980 time to fit residues: 9.7579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 126 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 127 optimal weight: 0.0020 chunk 231 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2277 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= 0.235 Angle : 0.551 8.865 31096 Z= 0.277 Chirality : 0.039 0.183 3476 Planarity : 0.004 0.044 3828 Dihedral : 10.904 117.835 3272 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.25 % Allowed : 15.48 % Favored : 83.26 % 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 : -0.41 (0.23), residues: 676 *********************** 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 390 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 360 time to evaluate : 2.642 Fit side-chains outliers start: 30 outliers final: 15 residues processed: 381 average time/residue: 0.3161 time to fit residues: 194.4620 Evaluate side-chains 358 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 343 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2098 time to fit residues: 9.2410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 232 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 91 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23004 Z= 0.399 Angle : 0.670 9.863 31096 Z= 0.335 Chirality : 0.043 0.210 3476 Planarity : 0.004 0.045 3828 Dihedral : 11.042 132.558 3272 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.96 % Allowed : 17.15 % Favored : 81.89 % 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: 1.89 (0.16), residues: 2644 helix: 1.82 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 680 *********************** 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 450 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 427 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 437 average time/residue: 0.3262 time to fit residues: 228.2641 Evaluate side-chains 387 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 373 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2173 time to fit residues: 9.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN B 91 ASN B 609 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23004 Z= 0.196 Angle : 0.551 9.460 31096 Z= 0.275 Chirality : 0.039 0.190 3476 Planarity : 0.004 0.045 3828 Dihedral : 10.683 123.353 3272 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.00 % Allowed : 18.49 % Favored : 80.51 % 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: 2.17 (0.17), residues: 2644 helix: 2.00 (0.12), residues: 1976 sheet: None (None), residues: 0 loop : -0.22 (0.24), residues: 668 *********************** 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 424 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 400 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 416 average time/residue: 0.3241 time to fit residues: 214.5977 Evaluate side-chains 359 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 347 time to evaluate : 2.447 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2253 time to fit residues: 8.4586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 189 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 144 optimal weight: 0.3980 chunk 258 optimal weight: 0.4980 chunk 161 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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** A 629 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN D 91 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23004 Z= 0.157 Angle : 0.539 7.855 31096 Z= 0.272 Chirality : 0.039 0.219 3476 Planarity : 0.004 0.046 3828 Dihedral : 10.398 119.380 3272 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.58 % Allowed : 19.03 % Favored : 80.38 % 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: 2.31 (0.16), residues: 2644 helix: 2.09 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.12 (0.24), residues: 672 *********************** 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 412 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 398 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 404 average time/residue: 0.3278 time to fit residues: 212.1193 Evaluate side-chains 352 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 348 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2013 time to fit residues: 5.2990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23004 Z= 0.269 Angle : 0.589 8.662 31096 Z= 0.298 Chirality : 0.041 0.241 3476 Planarity : 0.004 0.047 3828 Dihedral : 10.443 122.904 3272 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.00 % Allowed : 18.95 % Favored : 80.05 % 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: 2.23 (0.16), residues: 2644 helix: 2.06 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.23 (0.24), residues: 676 *********************** 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 392 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 368 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 381 average time/residue: 0.3305 time to fit residues: 198.8251 Evaluate side-chains 357 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 343 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2146 time to fit residues: 8.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 chunk 144 optimal weight: 0.0970 chunk 104 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23004 Z= 0.180 Angle : 0.564 9.309 31096 Z= 0.287 Chirality : 0.040 0.228 3476 Planarity : 0.004 0.048 3828 Dihedral : 10.052 119.176 3272 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.38 % Allowed : 19.87 % Favored : 79.76 % 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: 2.27 (0.16), residues: 2644 helix: 2.08 (0.12), residues: 1976 sheet: None (None), residues: 0 loop : -0.21 (0.25), residues: 668 *********************** 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 370 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 361 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 368 average time/residue: 0.3372 time to fit residues: 197.7531 Evaluate side-chains 345 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2059 time to fit residues: 6.1417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 120 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3522 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= 0.221 Angle : 0.586 9.461 31096 Z= 0.298 Chirality : 0.041 0.236 3476 Planarity : 0.004 0.048 3828 Dihedral : 9.782 119.471 3272 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.33 % Allowed : 20.16 % Favored : 79.51 % 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: 2.34 (0.17), residues: 2644 helix: 2.14 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.15 (0.24), residues: 680 ********************** 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 372 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 364 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 369 average time/residue: 0.3310 time to fit residues: 194.1963 Evaluate side-chains 349 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 343 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1970 time to fit residues: 5.8036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 196 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 218 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.160521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122919 restraints weight = 29513.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121093 restraints weight = 19571.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122879 restraints weight = 19044.939| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23004 Z= 0.184 Angle : 0.570 13.568 31096 Z= 0.291 Chirality : 0.040 0.230 3476 Planarity : 0.004 0.048 3828 Dihedral : 9.352 117.053 3272 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.13 % Allowed : 20.53 % Favored : 79.34 % 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: 2.38 (0.17), residues: 2644 helix: 2.16 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.14 (0.25), residues: 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.43 seconds wall clock time: 83 minutes 43.48 seconds (5023.48 seconds total)