Starting phenix.real_space_refine on Tue Mar 19 02:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqy_23491/03_2024/7lqy_23491_neut_updated.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 15132 2.51 5 N 3532 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 581": "NH1" <-> "NH2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 581": "NH1" <-> "NH2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B ARG 773": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 723": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 703": "NH1" <-> "NH2" Residue "D ARG 723": "NH1" <-> "NH2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "D ARG 773": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "B" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "C" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "D" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "A" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 420 Unusual residues: {' CL': 1, ' NA': 1, 'POV': 8, 'YBG': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 11.47, per 1000 atoms: 0.50 Number of scatterers: 22954 At special positions: 0 Unit cell: (122.96, 124.02, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 128 16.00 P 32 15.00 Na 1 11.00 O 4128 8.00 N 3532 7.00 C 15132 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.67 Conformation dependent library (CDL) restraints added in 4.1 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 51.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.520A pdb=" N ASP A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.550A pdb=" N ALA A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.688A pdb=" N LEU A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.670A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 418 through 428 removed outlier: 3.957A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 Processing helix chain 'A' and resid 471 through 498 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 543 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 544 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 548 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 551 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 577 removed outlier: 3.613A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 600 removed outlier: 3.805A pdb=" N VAL A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.505A pdb=" N LYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 672 Processing helix chain 'A' and resid 676 through 690 removed outlier: 3.613A pdb=" N ASN A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 3.539A pdb=" N SER A 713 " --> pdb=" O ASP A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 720' Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.520A pdb=" N ASP B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.550A pdb=" N ALA B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 270 removed outlier: 3.687A pdb=" N LEU B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.670A pdb=" N LYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 418 through 428 removed outlier: 3.957A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 Processing helix chain 'B' and resid 471 through 498 Processing helix chain 'B' and resid 513 through 533 Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL B 540 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 543 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 548 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 551 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 577 removed outlier: 3.612A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 600 removed outlier: 3.805A pdb=" N VAL B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.505A pdb=" N LYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 672 Processing helix chain 'B' and resid 676 through 690 removed outlier: 3.614A pdb=" N ASN B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 713 removed outlier: 3.539A pdb=" N SER B 713 " --> pdb=" O ASP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 720 " --> pdb=" O LYS B 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 715 through 720' Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.519A pdb=" N ASP C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.550A pdb=" N ALA C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 270 removed outlier: 3.687A pdb=" N LEU C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 321 removed outlier: 3.670A pdb=" N LYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 418 through 428 removed outlier: 3.956A pdb=" N ARG C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 455 Processing helix chain 'C' and resid 471 through 498 Processing helix chain 'C' and resid 513 through 533 Processing helix chain 'C' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL C 540 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET C 543 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL C 544 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 548 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP C 551 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 577 removed outlier: 3.612A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 600 removed outlier: 3.805A pdb=" N VAL C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.505A pdb=" N LYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 672 Processing helix chain 'C' and resid 676 through 690 removed outlier: 3.614A pdb=" N ASN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 713 removed outlier: 3.540A pdb=" N SER C 713 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG C 719 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 720 " --> pdb=" O LYS C 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 720' Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 159 through 165 Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.519A pdb=" N ASP D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.551A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 270 removed outlier: 3.688A pdb=" N LEU D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 321 removed outlier: 3.671A pdb=" N LYS D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 338 through 344 Processing helix chain 'D' and resid 348 through 354 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 418 through 428 removed outlier: 3.956A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 455 Processing helix chain 'D' and resid 471 through 498 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 537 through 556 removed outlier: 3.730A pdb=" N VAL D 540 " --> pdb=" O LYS D 537 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 543 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL D 544 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 548 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET D 549 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP D 551 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 577 removed outlier: 3.613A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 600 removed outlier: 3.804A pdb=" N VAL D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 644 removed outlier: 3.506A pdb=" N LYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 672 Processing helix chain 'D' and resid 676 through 690 removed outlier: 3.613A pdb=" N ASN D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 713 removed outlier: 3.539A pdb=" N SER D 713 " --> pdb=" O ASP D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 720 removed outlier: 3.853A pdb=" N ARG D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 720 " --> pdb=" O LYS D 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 715 through 720' Processing sheet with id= A, first strand: chain 'A' and resid 743 through 749 removed outlier: 4.026A pdb=" N TRP A 374 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 383 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR A 372 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 385 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 370 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 743 through 749 removed outlier: 4.027A pdb=" N TRP B 374 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 383 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B 372 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 385 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 370 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 743 through 749 removed outlier: 4.026A pdb=" N TRP C 374 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 383 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR C 372 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP C 385 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 370 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 743 through 749 removed outlier: 4.027A pdb=" N TRP D 374 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 383 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR D 372 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP D 385 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS D 370 " --> pdb=" O ASP D 385 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2400 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: 5.89 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3452 1.31 - 1.43: 6271 1.43 - 1.56: 13349 1.56 - 1.69: 124 1.69 - 1.81: 204 Bond restraints: 23400 Sorted by residual: bond pdb=" C31 POV B 902 " pdb=" O31 POV B 902 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C31 POV D 905 " pdb=" O31 POV D 905 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C31 POV C 902 " pdb=" O31 POV C 902 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C21 POV D 902 " pdb=" O21 POV D 902 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 23395 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.24: 260 104.24 - 111.69: 10336 111.69 - 119.14: 8646 119.14 - 126.59: 11820 126.59 - 134.04: 294 Bond angle restraints: 31356 Sorted by residual: angle pdb=" C10 YBG A 903 " pdb=" C1 YBG A 903 " pdb=" C2 YBG A 903 " ideal model delta sigma weight residual 152.65 120.26 32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C10 YBG C 903 " pdb=" C1 YBG C 903 " pdb=" C2 YBG C 903 " ideal model delta sigma weight residual 152.65 120.41 32.24 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C10 YBG D 906 " pdb=" C1 YBG D 906 " pdb=" C2 YBG D 906 " ideal model delta sigma weight residual 152.65 120.42 32.23 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C10 YBG B 903 " pdb=" C1 YBG B 903 " pdb=" C2 YBG B 903 " ideal model delta sigma weight residual 152.65 120.51 32.14 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C ARG A 430 " pdb=" N PHE A 431 " pdb=" CA PHE A 431 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 ... (remaining 31351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 13536 35.80 - 71.59: 563 71.59 - 107.39: 107 107.39 - 143.19: 46 143.19 - 178.98: 28 Dihedral angle restraints: 14280 sinusoidal: 6532 harmonic: 7748 Sorted by residual: dihedral pdb=" CA ARG A 624 " pdb=" C ARG A 624 " pdb=" N PRO A 625 " pdb=" CA PRO A 625 " ideal model delta harmonic sigma weight residual 180.00 147.28 32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA ARG B 624 " pdb=" C ARG B 624 " pdb=" N PRO B 625 " pdb=" CA PRO B 625 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.27e+01 dihedral pdb=" CA ARG D 624 " pdb=" C ARG D 624 " pdb=" N PRO D 625 " pdb=" CA PRO D 625 " ideal model delta harmonic sigma weight residual 180.00 147.32 32.68 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 14277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 3356 0.997 - 1.994: 0 1.994 - 2.991: 0 2.991 - 3.988: 0 3.988 - 4.985: 4 Chirality restraints: 3360 Sorted by residual: chirality pdb=" C38 YBG A 903 " pdb=" C39 YBG A 903 " pdb=" C43 YBG A 903 " pdb=" O8 YBG A 903 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C38 YBG B 903 " pdb=" C39 YBG B 903 " pdb=" C43 YBG B 903 " pdb=" O8 YBG B 903 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.18e+02 chirality pdb=" C38 YBG D 906 " pdb=" C39 YBG D 906 " pdb=" C43 YBG D 906 " pdb=" O8 YBG D 906 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.17e+02 ... (remaining 3357 not shown) Planarity restraints: 3796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 624 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO C 625 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 625 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 625 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 624 " 0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 625 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 625 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 624 " 0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 625 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " 0.046 5.00e-02 4.00e+02 ... (remaining 3793 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1960 2.73 - 3.27: 21823 3.27 - 3.81: 37358 3.81 - 4.36: 48562 4.36 - 4.90: 80870 Nonbonded interactions: 190573 Sorted by model distance: nonbonded pdb=" O PRO A 765 " pdb=" OH TYR B 201 " model vdw 2.186 2.440 nonbonded pdb=" O PRO C 765 " pdb=" OH TYR D 201 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR A 201 " pdb=" O PRO D 765 " model vdw 2.250 2.440 nonbonded pdb=" O PRO B 765 " pdb=" OH TYR C 201 " model vdw 2.251 2.440 nonbonded pdb=" N SER B 514 " pdb=" O6 YBG B 903 " model vdw 2.342 2.520 ... (remaining 190568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 111 through 779 or resid 901 through 902 or (resid 904 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 907 through 908 or (resid 909 and (name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)))) selection = (chain 'B' and (resid 111 through 779 or resid 901 through 902 or (resid 904 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 907 through 908 or (resid 909 and (name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)))) selection = (chain 'C' and (resid 111 through 779 or resid 901 through 902 or (resid 904 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 907 through 908 or (resid 909 and (name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)))) selection = (chain 'D' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 902 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or resid 904 through 905 or \ resid 907 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 0.960 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: 4.560 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 58.340 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.011 0.098 23400 Z= 0.657 Angle : 1.422 32.389 31356 Z= 0.662 Chirality : 0.179 4.985 3360 Planarity : 0.007 0.084 3796 Dihedral : 22.160 178.984 9296 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.28 % Rotamer: Outliers : 0.69 % Allowed : 5.32 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -5.23 (0.12), residues: 2620 helix: -4.09 (0.06), residues: 1456 sheet: -0.93 (0.60), residues: 96 loop : -2.52 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 699 HIS 0.008 0.002 HIS C 366 PHE 0.045 0.003 PHE A 431 TYR 0.014 0.002 TYR D 201 ARG 0.009 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 502 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8340 (m) cc_final: 0.7955 (t) REVERT: A 772 LYS cc_start: 0.7962 (tppp) cc_final: 0.7739 (tppt) REVERT: B 131 LEU cc_start: 0.8422 (tt) cc_final: 0.8115 (tp) REVERT: B 162 LYS cc_start: 0.8908 (tptm) cc_final: 0.8700 (tppp) REVERT: B 180 ASP cc_start: 0.8262 (m-30) cc_final: 0.8055 (m-30) REVERT: B 189 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7777 (tppt) REVERT: B 506 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7272 (tttm) REVERT: B 525 MET cc_start: 0.8359 (tpt) cc_final: 0.7917 (tpp) REVERT: B 772 LYS cc_start: 0.8038 (tppp) cc_final: 0.7808 (tppt) REVERT: C 133 SER cc_start: 0.8409 (m) cc_final: 0.7955 (t) REVERT: C 180 ASP cc_start: 0.7927 (m-30) cc_final: 0.7684 (m-30) REVERT: C 195 SER cc_start: 0.8130 (p) cc_final: 0.7618 (t) REVERT: C 506 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7359 (tttm) REVERT: C 525 MET cc_start: 0.8293 (tpt) cc_final: 0.7858 (tpp) REVERT: C 772 LYS cc_start: 0.8130 (tppp) cc_final: 0.7875 (tppt) REVERT: D 133 SER cc_start: 0.8367 (m) cc_final: 0.8021 (t) REVERT: D 180 ASP cc_start: 0.7813 (m-30) cc_final: 0.7530 (m-30) REVERT: D 506 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7524 (tttm) REVERT: D 619 ARG cc_start: 0.6047 (tpm-80) cc_final: 0.5818 (tpt170) REVERT: D 772 LYS cc_start: 0.8032 (tppp) cc_final: 0.7667 (tppt) outliers start: 16 outliers final: 5 residues processed: 510 average time/residue: 0.4172 time to fit residues: 313.0778 Evaluate side-chains 282 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 105 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 151 optimal weight: 0.0000 chunk 236 optimal weight: 0.6980 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 169 ASN A 225 ASN A 230 GLN A 261 ASN A 291 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 421 ASN A 697 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 129 GLN B 166 ASN B 169 ASN B 225 ASN B 230 GLN B 261 ASN B 291 HIS B 312 ASN B 421 ASN B 697 ASN C 129 GLN C 166 ASN C 169 ASN C 225 ASN C 230 GLN C 261 ASN C 291 HIS C 312 ASN C 421 ASN C 697 ASN D 129 GLN D 166 ASN D 169 ASN D 225 ASN D 230 GLN D 261 ASN D 291 HIS D 312 ASN D 360 GLN D 421 ASN D 697 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23400 Z= 0.153 Angle : 0.596 12.507 31356 Z= 0.297 Chirality : 0.039 0.239 3360 Planarity : 0.005 0.051 3796 Dihedral : 25.806 179.986 4238 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 2.79 % Allowed : 8.62 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 2620 helix: -1.57 (0.11), residues: 1456 sheet: 0.06 (0.61), residues: 84 loop : -2.09 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 699 HIS 0.003 0.001 HIS B 168 PHE 0.029 0.001 PHE A 431 TYR 0.013 0.001 TYR A 353 ARG 0.005 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 326 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7955 (m) cc_final: 0.7621 (t) REVERT: A 222 LEU cc_start: 0.8959 (mt) cc_final: 0.8697 (mp) REVERT: A 547 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 772 LYS cc_start: 0.8049 (tppp) cc_final: 0.7827 (tppt) REVERT: B 162 LYS cc_start: 0.8920 (tptm) cc_final: 0.8674 (tppp) REVERT: B 189 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7642 (mptt) REVERT: B 547 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8633 (tp) REVERT: B 772 LYS cc_start: 0.8118 (tppp) cc_final: 0.7885 (tppt) REVERT: C 195 SER cc_start: 0.8006 (p) cc_final: 0.7491 (t) REVERT: C 506 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7350 (tttm) REVERT: C 547 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8580 (tp) REVERT: C 772 LYS cc_start: 0.8340 (tppp) cc_final: 0.8061 (tppt) REVERT: D 133 SER cc_start: 0.8190 (m) cc_final: 0.7956 (t) REVERT: D 547 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 772 LYS cc_start: 0.8274 (tppp) cc_final: 0.7997 (tppt) outliers start: 65 outliers final: 43 residues processed: 381 average time/residue: 0.3520 time to fit residues: 207.6879 Evaluate side-chains 301 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 695 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 210 optimal weight: 0.3980 chunk 234 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 262 GLN A 312 ASN A 562 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 562 GLN B 654 ASN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 GLN ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN D 129 GLN D 360 GLN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23400 Z= 0.374 Angle : 0.658 11.930 31356 Z= 0.328 Chirality : 0.043 0.199 3360 Planarity : 0.004 0.044 3796 Dihedral : 23.968 179.835 4238 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 4.55 % Allowed : 9.99 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2620 helix: -0.37 (0.13), residues: 1488 sheet: -0.77 (0.55), residues: 84 loop : -1.93 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 754 HIS 0.004 0.001 HIS C 291 PHE 0.031 0.002 PHE A 431 TYR 0.012 0.002 TYR D 539 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 247 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8025 (m) cc_final: 0.7730 (t) REVERT: A 418 GLU cc_start: 0.7284 (tp30) cc_final: 0.6945 (tp30) REVERT: A 434 ARG cc_start: 0.7896 (tmt170) cc_final: 0.7668 (ttp80) REVERT: A 547 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 644 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 772 LYS cc_start: 0.8364 (tppp) cc_final: 0.8018 (tppt) REVERT: B 189 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7568 (mptt) REVERT: B 547 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8664 (tp) REVERT: B 772 LYS cc_start: 0.8350 (tppp) cc_final: 0.7993 (tppt) REVERT: C 189 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7574 (mptt) REVERT: C 218 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8832 (mm) REVERT: C 547 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8628 (tp) REVERT: C 772 LYS cc_start: 0.8401 (tppp) cc_final: 0.8091 (tppt) REVERT: D 133 SER cc_start: 0.8176 (m) cc_final: 0.7931 (t) REVERT: D 434 ARG cc_start: 0.7886 (tmt170) cc_final: 0.7591 (ttp80) REVERT: D 547 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8633 (tp) REVERT: D 714 PHE cc_start: 0.6764 (m-80) cc_final: 0.6285 (p90) REVERT: D 772 LYS cc_start: 0.8300 (tppp) cc_final: 0.7995 (tppt) outliers start: 106 outliers final: 74 residues processed: 333 average time/residue: 0.3496 time to fit residues: 181.3268 Evaluate side-chains 302 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 222 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 543 MET Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 0.0970 chunk 251 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN C 360 GLN C 380 HIS ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 380 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23400 Z= 0.142 Angle : 0.528 11.067 31356 Z= 0.264 Chirality : 0.037 0.156 3360 Planarity : 0.004 0.043 3796 Dihedral : 22.270 176.112 4238 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 3.26 % Allowed : 11.92 % Favored : 84.82 % 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 (0.16), residues: 2620 helix: 0.70 (0.14), residues: 1448 sheet: -0.53 (0.54), residues: 84 loop : -1.83 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 699 HIS 0.002 0.000 HIS D 291 PHE 0.029 0.001 PHE A 431 TYR 0.010 0.001 TYR C 586 ARG 0.006 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 245 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7964 (m) cc_final: 0.7564 (t) REVERT: A 218 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8790 (mm) REVERT: A 434 ARG cc_start: 0.7721 (tmt170) cc_final: 0.7487 (ttp80) REVERT: A 547 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 772 LYS cc_start: 0.8406 (tppp) cc_final: 0.8175 (tppt) REVERT: B 189 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7605 (tppt) REVERT: B 547 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8584 (tp) REVERT: B 772 LYS cc_start: 0.8341 (tppp) cc_final: 0.7994 (tppt) REVERT: C 131 LEU cc_start: 0.8364 (mt) cc_final: 0.7957 (pt) REVERT: C 189 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7588 (tppt) REVERT: C 547 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8618 (tp) REVERT: C 772 LYS cc_start: 0.8414 (tppp) cc_final: 0.8096 (tppt) REVERT: D 133 SER cc_start: 0.8191 (m) cc_final: 0.7941 (t) REVERT: D 434 ARG cc_start: 0.7747 (tmt170) cc_final: 0.7464 (ttp80) REVERT: D 547 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8642 (tp) REVERT: D 772 LYS cc_start: 0.8325 (tppp) cc_final: 0.8044 (tppt) outliers start: 76 outliers final: 51 residues processed: 304 average time/residue: 0.3518 time to fit residues: 166.2453 Evaluate side-chains 282 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 187 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23400 Z= 0.174 Angle : 0.534 10.789 31356 Z= 0.265 Chirality : 0.038 0.190 3360 Planarity : 0.003 0.040 3796 Dihedral : 21.239 175.167 4238 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.04 % Favored : 94.81 % Rotamer: Outliers : 3.64 % Allowed : 12.18 % Favored : 84.18 % 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: -0.09 (0.16), residues: 2620 helix: 1.09 (0.14), residues: 1468 sheet: -0.47 (0.53), residues: 84 loop : -1.71 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 754 HIS 0.002 0.001 HIS A 291 PHE 0.030 0.001 PHE A 431 TYR 0.007 0.001 TYR C 586 ARG 0.005 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 234 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7908 (m) cc_final: 0.7682 (t) REVERT: A 218 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 434 ARG cc_start: 0.7719 (tmt170) cc_final: 0.7486 (ttp80) REVERT: A 547 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8594 (tp) REVERT: A 772 LYS cc_start: 0.8398 (tppp) cc_final: 0.8156 (tppt) REVERT: B 189 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7685 (mptt) REVERT: B 434 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6465 (ptm-80) REVERT: B 547 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8591 (tp) REVERT: B 772 LYS cc_start: 0.8352 (tppp) cc_final: 0.8070 (tppt) REVERT: C 131 LEU cc_start: 0.8205 (mt) cc_final: 0.7787 (pt) REVERT: C 189 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7591 (tppt) REVERT: C 547 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8624 (tp) REVERT: C 772 LYS cc_start: 0.8392 (tppp) cc_final: 0.8083 (tppt) REVERT: D 133 SER cc_start: 0.8227 (m) cc_final: 0.8001 (t) REVERT: D 547 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8661 (tp) REVERT: D 564 MET cc_start: 0.8613 (mmm) cc_final: 0.8379 (mmm) REVERT: D 772 LYS cc_start: 0.8482 (tppp) cc_final: 0.8065 (tppt) outliers start: 85 outliers final: 66 residues processed: 303 average time/residue: 0.3583 time to fit residues: 169.8383 Evaluate side-chains 288 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 216 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 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 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23400 Z= 0.275 Angle : 0.582 12.326 31356 Z= 0.288 Chirality : 0.041 0.190 3360 Planarity : 0.004 0.048 3796 Dihedral : 20.933 174.226 4238 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 4.07 % Allowed : 12.09 % Favored : 83.83 % 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: -0.04 (0.16), residues: 2620 helix: 1.09 (0.14), residues: 1476 sheet: -0.70 (0.52), residues: 84 loop : -1.62 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 699 HIS 0.003 0.001 HIS B 291 PHE 0.030 0.002 PHE A 431 TYR 0.009 0.001 TYR D 586 ARG 0.008 0.001 ARG C 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 226 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7851 (m) cc_final: 0.7633 (t) REVERT: A 189 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7692 (mptt) REVERT: A 218 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 221 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8582 (tt) REVERT: A 418 GLU cc_start: 0.6943 (tp30) cc_final: 0.6649 (tp30) REVERT: A 434 ARG cc_start: 0.7751 (tmt170) cc_final: 0.7495 (ttp80) REVERT: A 547 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8627 (tp) REVERT: B 164 MET cc_start: 0.8538 (mmt) cc_final: 0.8331 (mmt) REVERT: B 189 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7849 (mmtm) REVERT: B 547 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 772 LYS cc_start: 0.8474 (tppp) cc_final: 0.8113 (tppt) REVERT: C 189 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7694 (tppt) REVERT: C 547 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 772 LYS cc_start: 0.8381 (tppp) cc_final: 0.8124 (tppt) REVERT: D 189 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7772 (tppt) REVERT: D 547 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8652 (tp) REVERT: D 772 LYS cc_start: 0.8483 (tppp) cc_final: 0.8106 (tppt) outliers start: 95 outliers final: 74 residues processed: 306 average time/residue: 0.3606 time to fit residues: 172.6081 Evaluate side-chains 299 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 219 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 156 optimal weight: 0.0270 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23400 Z= 0.150 Angle : 0.526 12.304 31356 Z= 0.261 Chirality : 0.038 0.225 3360 Planarity : 0.003 0.037 3796 Dihedral : 20.148 171.939 4238 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 3.52 % Allowed : 13.46 % Favored : 83.02 % 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: 0.28 (0.17), residues: 2620 helix: 1.47 (0.14), residues: 1456 sheet: -0.60 (0.52), residues: 84 loop : -1.60 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 754 HIS 0.002 0.001 HIS A 291 PHE 0.030 0.001 PHE D 431 TYR 0.009 0.001 TYR C 586 ARG 0.008 0.000 ARG C 430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 226 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7658 (mptt) REVERT: A 218 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8847 (mm) REVERT: A 221 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 434 ARG cc_start: 0.7705 (tmt170) cc_final: 0.7459 (ttp80) REVERT: A 547 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 554 MET cc_start: 0.8473 (ttm) cc_final: 0.8261 (tpp) REVERT: B 164 MET cc_start: 0.8370 (mmt) cc_final: 0.8155 (mmt) REVERT: B 189 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7785 (mmtm) REVERT: B 434 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6422 (ptm-80) REVERT: B 547 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8580 (tp) REVERT: B 554 MET cc_start: 0.8459 (ttm) cc_final: 0.8004 (tpp) REVERT: B 772 LYS cc_start: 0.8497 (tppp) cc_final: 0.8151 (tppt) REVERT: C 189 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7729 (tppt) REVERT: C 547 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8629 (tp) REVERT: C 772 LYS cc_start: 0.8403 (tppp) cc_final: 0.8090 (tppt) REVERT: D 189 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7689 (tppt) REVERT: D 547 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8616 (tp) REVERT: D 564 MET cc_start: 0.8514 (mmm) cc_final: 0.8288 (mmm) REVERT: D 772 LYS cc_start: 0.8467 (tppp) cc_final: 0.8094 (tppt) outliers start: 82 outliers final: 69 residues processed: 293 average time/residue: 0.3555 time to fit residues: 160.3254 Evaluate side-chains 293 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 217 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 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 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23400 Z= 0.166 Angle : 0.524 11.884 31356 Z= 0.260 Chirality : 0.038 0.226 3360 Planarity : 0.003 0.039 3796 Dihedral : 19.587 170.674 4238 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % Rotamer: Outliers : 3.77 % Allowed : 13.12 % Favored : 83.10 % 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: 0.28 (0.17), residues: 2620 helix: 1.45 (0.14), residues: 1488 sheet: -0.55 (0.52), residues: 84 loop : -1.68 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 754 HIS 0.002 0.001 HIS D 291 PHE 0.029 0.001 PHE D 431 TYR 0.009 0.001 TYR C 586 ARG 0.007 0.000 ARG D 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 220 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7616 (mptt) REVERT: A 218 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8813 (mm) REVERT: A 221 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8574 (tt) REVERT: A 547 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8604 (tp) REVERT: A 554 MET cc_start: 0.8537 (ttm) cc_final: 0.8302 (tpp) REVERT: B 434 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6469 (ptm-80) REVERT: B 547 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8634 (tp) REVERT: B 554 MET cc_start: 0.8456 (ttm) cc_final: 0.7954 (tpp) REVERT: B 772 LYS cc_start: 0.8532 (tppp) cc_final: 0.8196 (tppt) REVERT: C 189 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7730 (tppt) REVERT: C 547 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8616 (tp) REVERT: C 772 LYS cc_start: 0.8416 (tppp) cc_final: 0.8056 (tppt) REVERT: D 189 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7740 (tppt) REVERT: D 547 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8617 (tp) REVERT: D 564 MET cc_start: 0.8561 (mmm) cc_final: 0.8299 (mmm) REVERT: D 772 LYS cc_start: 0.8452 (tppp) cc_final: 0.8069 (tppt) outliers start: 88 outliers final: 73 residues processed: 292 average time/residue: 0.3402 time to fit residues: 154.3868 Evaluate side-chains 292 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 212 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23400 Z= 0.175 Angle : 0.529 11.984 31356 Z= 0.262 Chirality : 0.038 0.217 3360 Planarity : 0.003 0.038 3796 Dihedral : 19.042 168.215 4238 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.00 % Favored : 94.89 % Rotamer: Outliers : 3.52 % Allowed : 13.51 % Favored : 82.98 % 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: 0.35 (0.17), residues: 2620 helix: 1.55 (0.14), residues: 1476 sheet: -0.54 (0.51), residues: 84 loop : -1.67 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 754 HIS 0.002 0.001 HIS A 291 PHE 0.031 0.001 PHE A 431 TYR 0.009 0.001 TYR C 586 ARG 0.008 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 220 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7587 (mptt) REVERT: A 218 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 547 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 554 MET cc_start: 0.8544 (ttm) cc_final: 0.8294 (tpp) REVERT: A 718 MET cc_start: 0.6917 (mtt) cc_final: 0.6188 (mtm) REVERT: B 434 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6485 (ptm-80) REVERT: B 547 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8646 (tp) REVERT: B 554 MET cc_start: 0.8452 (ttm) cc_final: 0.7912 (tpp) REVERT: B 772 LYS cc_start: 0.8575 (tppp) cc_final: 0.8134 (tppt) REVERT: C 189 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7684 (tppt) REVERT: C 547 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8611 (tp) REVERT: C 772 LYS cc_start: 0.8441 (tppp) cc_final: 0.8128 (tppt) REVERT: D 189 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7780 (tppt) REVERT: D 547 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8617 (tp) REVERT: D 564 MET cc_start: 0.8636 (mmm) cc_final: 0.8351 (mmm) REVERT: D 772 LYS cc_start: 0.8465 (tppp) cc_final: 0.8107 (tppt) outliers start: 82 outliers final: 69 residues processed: 290 average time/residue: 0.3680 time to fit residues: 168.0762 Evaluate side-chains 289 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 214 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 5.9990 chunk 246 optimal weight: 0.0470 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 159 optimal weight: 0.0570 chunk 126 optimal weight: 6.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS C 412 HIS C 630 ASN D 412 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23400 Z= 0.126 Angle : 0.507 11.957 31356 Z= 0.251 Chirality : 0.037 0.198 3360 Planarity : 0.003 0.038 3796 Dihedral : 18.099 165.371 4238 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.87 % Allowed : 14.15 % Favored : 82.98 % 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: 0.46 (0.17), residues: 2620 helix: 1.57 (0.14), residues: 1512 sheet: -0.35 (0.51), residues: 84 loop : -1.65 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 754 HIS 0.002 0.000 HIS A 291 PHE 0.030 0.001 PHE D 431 TYR 0.009 0.001 TYR C 557 ARG 0.007 0.000 ARG A 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 233 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8216 (mmt) cc_final: 0.7990 (mmm) REVERT: A 189 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7511 (mptt) REVERT: A 218 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 414 MET cc_start: 0.8980 (mtm) cc_final: 0.8708 (mtp) REVERT: A 547 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 554 MET cc_start: 0.8504 (ttm) cc_final: 0.8276 (tpp) REVERT: A 718 MET cc_start: 0.6993 (mtt) cc_final: 0.6170 (mtt) REVERT: B 547 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 554 MET cc_start: 0.8471 (ttm) cc_final: 0.7934 (tpp) REVERT: B 772 LYS cc_start: 0.8565 (tppp) cc_final: 0.8128 (tppt) REVERT: C 171 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7750 (tm-30) REVERT: C 189 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7666 (tppt) REVERT: C 414 MET cc_start: 0.8954 (mtm) cc_final: 0.8711 (mtp) REVERT: C 547 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8585 (tp) REVERT: C 772 LYS cc_start: 0.8425 (tppp) cc_final: 0.8131 (tppt) REVERT: D 117 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7574 (tpp-160) REVERT: D 189 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7657 (tppt) REVERT: D 547 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8576 (tp) REVERT: D 718 MET cc_start: 0.6555 (mtt) cc_final: 0.6282 (mtt) REVERT: D 748 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7340 (mt-10) REVERT: D 772 LYS cc_start: 0.8493 (tppp) cc_final: 0.8120 (tppt) outliers start: 67 outliers final: 54 residues processed: 294 average time/residue: 0.3354 time to fit residues: 154.9436 Evaluate side-chains 279 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 767 ASN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 57 optimal weight: 0.0030 chunk 206 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 212 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099623 restraints weight = 35256.872| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.34 r_work: 0.3116 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23400 Z= 0.122 Angle : 0.500 11.956 31356 Z= 0.248 Chirality : 0.037 0.223 3360 Planarity : 0.003 0.038 3796 Dihedral : 17.421 162.926 4238 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.40 % Allowed : 14.71 % Favored : 82.89 % 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: 0.59 (0.17), residues: 2620 helix: 1.68 (0.14), residues: 1512 sheet: -0.24 (0.51), residues: 84 loop : -1.60 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 754 HIS 0.002 0.000 HIS A 291 PHE 0.031 0.001 PHE D 431 TYR 0.008 0.001 TYR C 586 ARG 0.008 0.000 ARG D 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4759.05 seconds wall clock time: 87 minutes 2.95 seconds (5222.95 seconds total)