Starting phenix.real_space_refine on Sat Feb 17 06:45:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agc_15420/02_2024/8agc_15420_updated.pdb" } resolution = 3.1 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= 0.002 sd= 0.062 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 11681 2.51 5 N 2758 2.21 5 O 3259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A ARG 649": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E GLU 357": "OE1" <-> "OE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H GLU 269": "OE1" <-> "OE2" Residue "H PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 295": "NH1" <-> "NH2" Residue "H GLU 301": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17764 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5594 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 671} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 883 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3537 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 24, 'TRANS': 413} Chain breaks: 1 Chain: "F" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1892 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 15, 'TRANS': 242} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3201 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1050 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 43 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'DAB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'GLC': 3, 'MAN': 5, 'NAG': 1, 'NDG': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {' MG': 1, 'CPL': 1, 'ELU': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'323': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.80, per 1000 atoms: 0.55 Number of scatterers: 17764 At special positions: 0 Unit cell: (124.1, 117.3, 154.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 8 15.00 Mg 1 11.99 O 3259 8.00 N 2758 7.00 C 11681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN I 5 " - " MAN I 6 " " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " GLC L 8 " - " GLC L 9 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA L 3 " - " MAN L 4 " " MAN L 6 " - " GLC L 7 " " GLC L 7 " - " GLC L 8 " " MAN L 10 " - " MAN L 11 " ALPHA1-6 " BMA I 3 " - " MAN I 7 " " BMA L 3 " - " MAN L 10 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NDG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG G 501 " - " ASN G 332 " " NAG G 502 " - " ASN G 60 " " NAG I 1 " - " ASN A 539 " " NAG J 1 " - " ASN E 336 " " NAG K 1 " - " ASN E 400 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.79 Conformation dependent library (CDL) restraints added in 3.0 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 17 sheets defined 41.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 38 removed outlier: 4.462A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 111 through 136 removed outlier: 5.043A pdb=" N ALA A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 4.091A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.882A pdb=" N ILE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 4.389A pdb=" N ARG A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.441A pdb=" N THR A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 Processing helix chain 'A' and resid 211 through 227 removed outlier: 5.073A pdb=" N ILE A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 233 through 250 Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 264 through 289 removed outlier: 4.638A pdb=" N ALA A 268 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 269 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 275 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 276 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 280 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 287 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN A 288 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 319 removed outlier: 3.926A pdb=" N VAL A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 309 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 366 through 379 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 383 through 401 Processing helix chain 'A' and resid 403 through 428 removed outlier: 4.031A pdb=" N LEU A 407 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 408 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.868A pdb=" N LEU A 421 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 472 Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 517 through 526 removed outlier: 4.940A pdb=" N TYR A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN A 522 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 554 through 564 Processing helix chain 'A' and resid 583 through 597 removed outlier: 3.772A pdb=" N PHE A 587 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 589 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 591 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 594 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'B' and resid 4 through 32 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 22 through 46 Proline residue: C 26 - end of helix removed outlier: 4.097A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 82 Processing helix chain 'D' and resid 23 through 40 removed outlier: 3.964A pdb=" N LYS D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 67 removed outlier: 4.674A pdb=" N ILE D 47 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.633A pdb=" N ILE D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D 84 " --> pdb=" O GLY D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 3.889A pdb=" N PHE D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.710A pdb=" N LYS E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 443 through 446 No H-bonds generated for 'chain 'E' and resid 443 through 446' Processing helix chain 'E' and resid 448 through 468 Processing helix chain 'F' and resid 119 through 127 Processing helix chain 'F' and resid 192 through 214 removed outlier: 3.612A pdb=" N LEU F 214 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 251 removed outlier: 3.720A pdb=" N VAL F 241 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE F 243 " --> pdb=" O ILE F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 280 removed outlier: 3.683A pdb=" N SER F 263 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 264 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.703A pdb=" N THR F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 50 removed outlier: 5.676A pdb=" N VAL G 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR G 43 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 93 No H-bonds generated for 'chain 'G' and resid 90 through 93' Processing helix chain 'G' and resid 96 through 104 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 248 through 257 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 390 through 415 Processing helix chain 'H' and resid 217 through 233 Processing helix chain 'H' and resid 237 through 240 No H-bonds generated for 'chain 'H' and resid 237 through 240' Processing helix chain 'H' and resid 267 through 289 removed outlier: 3.912A pdb=" N GLN H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 298 Processing helix chain 'H' and resid 306 through 334 removed outlier: 3.609A pdb=" N LYS H 334 " --> pdb=" O VAL H 330 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.126A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 645 through 647 Processing sheet with id= C, first strand: chain 'E' and resid 173 through 178 removed outlier: 8.570A pdb=" N SER E 174 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR E 36 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR E 176 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG E 38 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE E 178 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE E 40 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR E 54 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR E 36 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU E 52 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG E 38 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR E 50 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE E 40 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 48 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 47 " --> pdb=" O TYR E 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 65 through 70 removed outlier: 4.587A pdb=" N TYR E 114 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN E 93 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 154 through 160 removed outlier: 4.591A pdb=" N ALA E 221 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 400 through 406 removed outlier: 8.439A pdb=" N GLU E 378 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 236 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER E 380 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG E 238 " --> pdb=" O SER E 380 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE E 382 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 240 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU E 256 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU E 236 " --> pdb=" O TYR E 254 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR E 254 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG E 238 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU E 252 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE E 240 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN E 250 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU E 242 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 248 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 291 through 294 Processing sheet with id= H, first strand: chain 'E' and resid 349 through 351 removed outlier: 5.981A pdb=" N ASP E 440 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE E 389 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 68 through 70 Processing sheet with id= J, first strand: chain 'F' and resid 94 through 96 removed outlier: 3.598A pdb=" N LEU F 154 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 136 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU F 152 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU F 138 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE F 150 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 55 through 58 removed outlier: 6.799A pdb=" N ASN G 78 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU G 29 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE G 80 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN G 108 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL G 81 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU G 110 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 131 through 133 Processing sheet with id= M, first strand: chain 'G' and resid 138 through 141 removed outlier: 3.712A pdb=" N VAL G 139 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 263 through 267 removed outlier: 4.144A pdb=" N VAL G 263 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR G 292 " --> pdb=" O THR G 341 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 270 through 273 Processing sheet with id= P, first strand: chain 'G' and resid 297 through 299 Processing sheet with id= Q, first strand: chain 'G' and resid 367 through 375 removed outlier: 4.197A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 1881 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: 5.95 Time building geometry restraints manager: 8.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2711 1.30 - 1.43: 5223 1.43 - 1.56: 10141 1.56 - 1.68: 51 1.68 - 1.81: 96 Bond restraints: 18222 Sorted by residual: bond pdb=" C7 323 P 101 " pdb=" N2 323 P 101 " ideal model delta sigma weight residual 1.342 1.497 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C4 323 P 101 " pdb=" O1 323 P 101 " ideal model delta sigma weight residual 1.344 1.491 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C3 323 P 101 " pdb=" O1 323 P 101 " ideal model delta sigma weight residual 1.344 1.463 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C11 CPL E 501 " pdb=" O3 CPL E 501 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 CPL C 101 " pdb=" O2 CPL C 101 " ideal model delta sigma weight residual 1.332 1.427 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 18217 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.08: 341 105.08 - 112.49: 9618 112.49 - 119.89: 6341 119.89 - 127.30: 8212 127.30 - 134.70: 208 Bond angle restraints: 24720 Sorted by residual: angle pdb=" C14 ELU A1001 " pdb=" C13 ELU A1001 " pdb=" C15 ELU A1001 " ideal model delta sigma weight residual 68.19 118.94 -50.75 3.00e+00 1.11e-01 2.86e+02 angle pdb=" C12 ELU A1001 " pdb=" C13 ELU A1001 " pdb=" C15 ELU A1001 " ideal model delta sigma weight residual 85.86 123.16 -37.30 3.00e+00 1.11e-01 1.55e+02 angle pdb=" C12 ELU A1001 " pdb=" C13 ELU A1001 " pdb=" C14 ELU A1001 " ideal model delta sigma weight residual 152.70 117.88 34.82 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C3 MAN L 4 " pdb=" C2 MAN L 4 " pdb=" O2 MAN L 4 " ideal model delta sigma weight residual 111.77 97.68 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O11 PTY A1003 " pdb=" P1 PTY A1003 " pdb=" O14 PTY A1003 " ideal model delta sigma weight residual 92.90 106.30 -13.40 3.00e+00 1.11e-01 2.00e+01 ... (remaining 24715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 10523 35.84 - 71.69: 369 71.69 - 107.53: 68 107.53 - 143.37: 18 143.37 - 179.21: 3 Dihedral angle restraints: 10981 sinusoidal: 4665 harmonic: 6316 Sorted by residual: dihedral pdb=" N CPL F 301 " pdb=" C4 CPL F 301 " pdb=" C5 CPL F 301 " pdb=" O4P CPL F 301 " ideal model delta sinusoidal sigma weight residual -71.08 108.13 -179.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N CPL A1002 " pdb=" C4 CPL A1002 " pdb=" C5 CPL A1002 " pdb=" O4P CPL A1002 " ideal model delta sinusoidal sigma weight residual -71.08 80.85 -151.93 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" N CPL C 101 " pdb=" C4 CPL C 101 " pdb=" C5 CPL C 101 " pdb=" O4P CPL C 101 " ideal model delta sinusoidal sigma weight residual -71.08 79.10 -150.18 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 10978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2776 0.141 - 0.282: 39 0.282 - 0.423: 5 0.423 - 0.564: 1 0.564 - 0.705: 2 Chirality restraints: 2823 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 400 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG G 501 " pdb=" ND2 ASN G 332 " pdb=" C2 NAG G 501 " pdb=" O5 NAG G 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" C1 NAG G 502 " pdb=" ND2 ASN G 60 " pdb=" C2 NAG G 502 " pdb=" O5 NAG G 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 2820 not shown) Planarity restraints: 3032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 323 P 101 " 0.160 2.00e-02 2.50e+03 3.03e-01 4.36e+03 pdb=" C10 323 P 101 " -0.012 2.00e-02 2.50e+03 pdb=" C11 323 P 101 " -0.077 2.00e-02 2.50e+03 pdb=" C12 323 P 101 " -0.039 2.00e-02 2.50e+03 pdb=" C13 323 P 101 " 0.062 2.00e-02 2.50e+03 pdb=" C16 323 P 101 " -0.939 2.00e-02 2.50e+03 pdb=" C17 323 P 101 " 0.710 2.00e-02 2.50e+03 pdb=" C18 323 P 101 " 0.315 2.00e-02 2.50e+03 pdb=" C2 323 P 101 " 0.090 2.00e-02 2.50e+03 pdb=" C3 323 P 101 " 0.126 2.00e-02 2.50e+03 pdb=" C4 323 P 101 " 0.089 2.00e-02 2.50e+03 pdb=" C5 323 P 101 " 0.054 2.00e-02 2.50e+03 pdb=" C6 323 P 101 " -0.011 2.00e-02 2.50e+03 pdb=" C7 323 P 101 " -0.145 2.00e-02 2.50e+03 pdb=" C8 323 P 101 " -0.182 2.00e-02 2.50e+03 pdb=" C9 323 P 101 " -0.084 2.00e-02 2.50e+03 pdb=" N1 323 P 101 " -0.098 2.00e-02 2.50e+03 pdb=" N2 323 P 101 " -0.252 2.00e-02 2.50e+03 pdb=" O1 323 P 101 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL F 301 " 0.097 2.00e-02 2.50e+03 2.19e-01 4.81e+02 pdb=" C39 CPL F 301 " -0.291 2.00e-02 2.50e+03 pdb=" C40 CPL F 301 " 0.297 2.00e-02 2.50e+03 pdb=" C41 CPL F 301 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 CPL A1002 " 0.096 2.00e-02 2.50e+03 2.16e-01 4.65e+02 pdb=" C42 CPL A1002 " -0.288 2.00e-02 2.50e+03 pdb=" C43 CPL A1002 " 0.290 2.00e-02 2.50e+03 pdb=" C44 CPL A1002 " -0.099 2.00e-02 2.50e+03 ... (remaining 3029 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 531 2.69 - 3.24: 17152 3.24 - 3.80: 27092 3.80 - 4.35: 36602 4.35 - 4.90: 62178 Nonbonded interactions: 143555 Sorted by model distance: nonbonded pdb=" OD2 ASP A 166 " pdb="MG MG A1004 " model vdw 2.139 2.170 nonbonded pdb=" OH TYR D 34 " pdb=" OD2 ASP D 48 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR A 64 " pdb=" OD1 ASP G 381 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASP G 333 " pdb=" N SER G 334 " model vdw 2.238 2.520 nonbonded pdb=" O SER G 330 " pdb=" OG SER G 330 " model vdw 2.239 2.440 ... (remaining 143550 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 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 13.510 Check model and map are aligned: 0.270 Set scattering table: 0.200 Process input model: 51.700 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 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: 73.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.155 18222 Z= 0.579 Angle : 1.062 50.747 24720 Z= 0.520 Chirality : 0.058 0.705 2823 Planarity : 0.011 0.303 3027 Dihedral : 19.292 179.213 6903 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 3.53 % Allowed : 12.77 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2124 helix: 0.31 (0.17), residues: 898 sheet: -0.54 (0.26), residues: 391 loop : -1.99 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP G 299 HIS 0.013 0.002 HIS A 364 PHE 0.039 0.002 PHE A 370 TYR 0.034 0.002 TYR A 52 ARG 0.007 0.001 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 278 time to evaluate : 2.094 Fit side-chains revert: symmetry clash REVERT: A 333 TRP cc_start: 0.7499 (t60) cc_final: 0.7269 (t60) REVERT: B 29 ASP cc_start: 0.8554 (t70) cc_final: 0.8273 (t0) REVERT: C 27 LYS cc_start: 0.8065 (mttp) cc_final: 0.7713 (ptmm) REVERT: D 31 LYS cc_start: 0.8765 (tttt) cc_final: 0.8556 (tttm) REVERT: D 45 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8165 (ttmt) REVERT: E 195 LEU cc_start: 0.8398 (tp) cc_final: 0.8192 (tt) REVERT: F 98 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6809 (pt0) REVERT: G 392 SER cc_start: 0.8907 (m) cc_final: 0.8651 (p) REVERT: H 273 MET cc_start: 0.8761 (mmm) cc_final: 0.8432 (mmp) outliers start: 65 outliers final: 22 residues processed: 332 average time/residue: 0.3188 time to fit residues: 156.9218 Evaluate side-chains 188 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 432 ASN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 100 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 216 ASN A 221 HIS A 351 HIS A 352 GLN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 564 HIS A 642 ASN A 645 GLN A 652 GLN A 653 GLN A 674 ASN C 80 ASN D 37 GLN D 108 ASN E 93 ASN E 121 ASN E 201 ASN E 232 GLN E 235 ASN E 343 ASN E 367 ASN E 416 HIS F 66 GLN F 79 GLN F 181 HIS G 32 GLN G 105 ASN G 108 ASN G 156 ASN G 214 GLN G 222 GLN G 225 ASN G 226 ASN G 242 ASN G 246 ASN G 247 GLN G 271 HIS G 318 GLN G 337 GLN H 238 ASN H 271 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18222 Z= 0.157 Angle : 0.608 21.745 24720 Z= 0.301 Chirality : 0.044 0.322 2823 Planarity : 0.004 0.046 3027 Dihedral : 16.894 148.875 3079 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.12 % Favored : 97.83 % Rotamer: Outliers : 2.34 % Allowed : 15.60 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2124 helix: 0.82 (0.17), residues: 914 sheet: -0.16 (0.27), residues: 400 loop : -1.57 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 299 HIS 0.007 0.001 HIS B 26 PHE 0.023 0.001 PHE H 293 TYR 0.018 0.001 TYR F 108 ARG 0.004 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 2.149 Fit side-chains REVERT: A 333 TRP cc_start: 0.7418 (t60) cc_final: 0.7198 (t60) REVERT: B 29 ASP cc_start: 0.8510 (t70) cc_final: 0.8205 (t0) REVERT: D 31 LYS cc_start: 0.8678 (tttt) cc_final: 0.8278 (tttm) REVERT: D 45 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8043 (ttmt) REVERT: F 98 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6767 (pt0) REVERT: G 392 SER cc_start: 0.8652 (m) cc_final: 0.8451 (p) outliers start: 43 outliers final: 25 residues processed: 222 average time/residue: 0.3044 time to fit residues: 103.3379 Evaluate side-chains 180 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 206 optimal weight: 0.0470 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS B 26 HIS D 97 GLN D 127 HIS F 123 GLN F 222 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18222 Z= 0.289 Angle : 0.622 21.873 24720 Z= 0.306 Chirality : 0.044 0.326 2823 Planarity : 0.004 0.044 3027 Dihedral : 14.578 131.512 3049 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.48 % Allowed : 14.78 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2124 helix: 1.11 (0.17), residues: 914 sheet: -0.02 (0.27), residues: 396 loop : -1.37 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 299 HIS 0.005 0.001 HIS B 26 PHE 0.028 0.002 PHE A 370 TYR 0.021 0.002 TYR E 409 ARG 0.006 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 162 time to evaluate : 2.328 Fit side-chains REVERT: A 78 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8993 (mt) REVERT: A 494 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7932 (t0) REVERT: B 29 ASP cc_start: 0.8542 (t70) cc_final: 0.8263 (t0) REVERT: C 27 LYS cc_start: 0.8242 (mttp) cc_final: 0.7684 (ptmm) REVERT: D 31 LYS cc_start: 0.8559 (tttt) cc_final: 0.8350 (tttm) REVERT: D 45 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8133 (ttmt) REVERT: G 392 SER cc_start: 0.8773 (m) cc_final: 0.8569 (p) REVERT: H 255 MET cc_start: 0.6953 (ptt) cc_final: 0.6714 (ptt) REVERT: H 271 GLN cc_start: 0.8895 (mp10) cc_final: 0.8596 (mp10) outliers start: 64 outliers final: 46 residues processed: 208 average time/residue: 0.3254 time to fit residues: 103.4991 Evaluate side-chains 202 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 154 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 199 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18222 Z= 0.165 Angle : 0.554 21.805 24720 Z= 0.269 Chirality : 0.042 0.295 2823 Planarity : 0.004 0.040 3027 Dihedral : 13.379 129.603 3049 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.21 % Allowed : 15.60 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2124 helix: 1.28 (0.17), residues: 923 sheet: -0.16 (0.27), residues: 408 loop : -1.16 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.014 0.001 HIS A 542 PHE 0.021 0.001 PHE H 293 TYR 0.021 0.001 TYR D 41 ARG 0.004 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 2.211 Fit side-chains REVERT: A 78 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8906 (mt) REVERT: A 494 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7858 (t0) REVERT: B 29 ASP cc_start: 0.8538 (t70) cc_final: 0.8268 (t0) REVERT: D 31 LYS cc_start: 0.8595 (tttt) cc_final: 0.8325 (tttm) REVERT: D 45 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8129 (ttmt) REVERT: D 130 ASN cc_start: 0.8692 (t0) cc_final: 0.8379 (t0) REVERT: G 51 ASN cc_start: 0.8359 (p0) cc_final: 0.8122 (p0) outliers start: 59 outliers final: 45 residues processed: 211 average time/residue: 0.3044 time to fit residues: 96.9193 Evaluate side-chains 206 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 173 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS D 97 GLN E 199 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18222 Z= 0.287 Angle : 0.579 21.788 24720 Z= 0.286 Chirality : 0.043 0.261 2823 Planarity : 0.004 0.039 3027 Dihedral : 12.983 129.227 3049 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.64 % Allowed : 16.20 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2124 helix: 1.34 (0.17), residues: 923 sheet: -0.13 (0.27), residues: 400 loop : -1.15 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 299 HIS 0.004 0.001 HIS G 138 PHE 0.027 0.001 PHE H 293 TYR 0.021 0.001 TYR E 409 ARG 0.006 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 160 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8954 (mt) REVERT: A 494 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7980 (t0) REVERT: B 29 ASP cc_start: 0.8563 (t70) cc_final: 0.8286 (t0) REVERT: C 27 LYS cc_start: 0.8282 (mttp) cc_final: 0.7681 (ptmm) REVERT: D 31 LYS cc_start: 0.8605 (tttt) cc_final: 0.8318 (tttm) REVERT: D 45 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8203 (ttmt) REVERT: E 473 ASN cc_start: 0.5959 (t0) cc_final: 0.5556 (m-40) REVERT: G 51 ASN cc_start: 0.8381 (p0) cc_final: 0.8094 (p0) REVERT: H 255 MET cc_start: 0.7075 (ptt) cc_final: 0.6807 (ptt) outliers start: 67 outliers final: 55 residues processed: 207 average time/residue: 0.3034 time to fit residues: 95.3619 Evaluate side-chains 212 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 155 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 199 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18222 Z= 0.166 Angle : 0.532 21.802 24720 Z= 0.260 Chirality : 0.042 0.255 2823 Planarity : 0.004 0.037 3027 Dihedral : 12.376 126.983 3049 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.32 % Allowed : 16.79 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2124 helix: 1.52 (0.17), residues: 916 sheet: -0.20 (0.27), residues: 409 loop : -1.11 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.007 0.001 HIS A 542 PHE 0.024 0.001 PHE H 293 TYR 0.018 0.001 TYR D 41 ARG 0.005 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 2.374 Fit side-chains revert: symmetry clash REVERT: A 494 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7935 (t0) REVERT: B 29 ASP cc_start: 0.8567 (t70) cc_final: 0.8301 (t0) REVERT: D 45 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8108 (ttmt) REVERT: E 473 ASN cc_start: 0.5945 (t0) cc_final: 0.5564 (m-40) REVERT: G 51 ASN cc_start: 0.8397 (p0) cc_final: 0.8103 (p0) REVERT: H 255 MET cc_start: 0.7010 (ptt) cc_final: 0.6742 (ptt) outliers start: 61 outliers final: 49 residues processed: 205 average time/residue: 0.3025 time to fit residues: 95.1433 Evaluate side-chains 205 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 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 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 199 ASN G 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18222 Z= 0.146 Angle : 0.521 21.747 24720 Z= 0.251 Chirality : 0.041 0.250 2823 Planarity : 0.004 0.036 3027 Dihedral : 11.582 124.989 3049 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.77 % Allowed : 17.72 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2124 helix: 1.67 (0.17), residues: 921 sheet: 0.01 (0.27), residues: 390 loop : -1.01 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.006 0.001 HIS A 542 PHE 0.030 0.001 PHE H 293 TYR 0.016 0.001 TYR H 235 ARG 0.005 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8894 (mt) REVERT: A 494 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7912 (t0) REVERT: B 29 ASP cc_start: 0.8567 (t70) cc_final: 0.8305 (t0) REVERT: D 45 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8053 (ttmt) REVERT: G 51 ASN cc_start: 0.8358 (p0) cc_final: 0.8112 (p0) outliers start: 51 outliers final: 44 residues processed: 204 average time/residue: 0.3384 time to fit residues: 103.6720 Evaluate side-chains 198 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 97 GLN E 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18222 Z= 0.165 Angle : 0.529 21.747 24720 Z= 0.255 Chirality : 0.041 0.253 2823 Planarity : 0.004 0.035 3027 Dihedral : 11.298 126.054 3048 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.88 % Allowed : 17.50 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2124 helix: 1.69 (0.17), residues: 921 sheet: 0.12 (0.28), residues: 385 loop : -0.97 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 364 PHE 0.028 0.001 PHE H 293 TYR 0.028 0.001 TYR D 41 ARG 0.007 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 151 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8909 (mt) REVERT: A 494 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7908 (t0) REVERT: B 29 ASP cc_start: 0.8577 (t70) cc_final: 0.8315 (t0) REVERT: D 45 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8073 (ttmt) REVERT: G 51 ASN cc_start: 0.8356 (p0) cc_final: 0.8103 (p0) outliers start: 53 outliers final: 47 residues processed: 192 average time/residue: 0.2928 time to fit residues: 85.1775 Evaluate side-chains 199 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 57 optimal weight: 0.0030 chunk 170 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 0.0980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 ASN H 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18222 Z= 0.122 Angle : 0.510 21.719 24720 Z= 0.244 Chirality : 0.041 0.247 2823 Planarity : 0.004 0.035 3027 Dihedral : 10.578 123.260 3048 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.17 % Allowed : 18.26 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2124 helix: 1.77 (0.17), residues: 920 sheet: 0.21 (0.28), residues: 383 loop : -0.92 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.003 0.001 HIS A 364 PHE 0.028 0.001 PHE H 293 TYR 0.013 0.001 TYR H 235 ARG 0.007 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 2.102 Fit side-chains revert: symmetry clash REVERT: A 494 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7960 (t0) REVERT: B 29 ASP cc_start: 0.8573 (t70) cc_final: 0.8319 (t0) REVERT: D 45 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8063 (ttmt) REVERT: E 470 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (mp) REVERT: G 51 ASN cc_start: 0.8380 (p0) cc_final: 0.8105 (p0) REVERT: H 255 MET cc_start: 0.7000 (ptt) cc_final: 0.6733 (ptt) outliers start: 40 outliers final: 31 residues processed: 192 average time/residue: 0.3282 time to fit residues: 95.0927 Evaluate side-chains 185 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS D 37 GLN D 97 GLN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18222 Z= 0.287 Angle : 0.577 21.794 24720 Z= 0.281 Chirality : 0.043 0.259 2823 Planarity : 0.004 0.036 3027 Dihedral : 10.870 129.892 3048 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.17 % Allowed : 18.80 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2124 helix: 1.63 (0.17), residues: 917 sheet: 0.06 (0.27), residues: 393 loop : -0.94 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 299 HIS 0.004 0.001 HIS E 302 PHE 0.029 0.001 PHE A 370 TYR 0.019 0.001 TYR E 409 ARG 0.006 0.000 ARG F 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.921 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8971 (mt) REVERT: A 494 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 29 ASP cc_start: 0.8586 (t70) cc_final: 0.8319 (t0) REVERT: C 27 LYS cc_start: 0.8323 (mttp) cc_final: 0.7626 (ptmm) REVERT: D 45 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8096 (ttmt) REVERT: G 51 ASN cc_start: 0.8362 (p0) cc_final: 0.8095 (p0) REVERT: G 345 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8934 (mm) outliers start: 40 outliers final: 35 residues processed: 178 average time/residue: 0.3186 time to fit residues: 85.3681 Evaluate side-chains 182 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 146 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 97 GLN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.079950 restraints weight = 29073.485| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.23 r_work: 0.2821 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18222 Z= 0.149 Angle : 0.531 21.829 24720 Z= 0.257 Chirality : 0.041 0.245 2823 Planarity : 0.004 0.035 3027 Dihedral : 10.505 126.475 3048 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.07 % Allowed : 18.91 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2124 helix: 1.66 (0.17), residues: 921 sheet: 0.13 (0.28), residues: 386 loop : -0.92 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 517 HIS 0.003 0.001 HIS G 138 PHE 0.028 0.001 PHE H 293 TYR 0.016 0.001 TYR H 235 ARG 0.006 0.000 ARG F 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4005.69 seconds wall clock time: 73 minutes 35.97 seconds (4415.97 seconds total)