Starting phenix.real_space_refine on Mon Mar 18 16:57:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9v_0380/03_2024/6n9v_0380_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.057 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 Zn 1 6.06 5 P 50 5.49 5 Mg 7 5.21 5 S 124 5.16 5 C 13409 2.51 5 N 3763 2.21 5 O 4172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 255": "NH1" <-> "NH2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H ARG 547": "NH1" <-> "NH2" Residue "H ARG 566": "NH1" <-> "NH2" Residue "H ARG 591": "NH1" <-> "NH2" Residue "H ARG 599": "NH1" <-> "NH2" Residue "H TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 687": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21526 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1955 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain breaks: 6 Chain: "B" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2117 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 3 Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2097 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 4, 'TRANS': 267} Chain breaks: 3 Chain: "D" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2056 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 262} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3758 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 472} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "F" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3549 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 446} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 546 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, ' ZN': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8294 SG CYS E 17 81.080 73.616 148.480 1.00182.63 S ATOM 8316 SG CYS E 20 79.419 75.737 150.798 1.00187.79 S ATOM 8429 SG CYS E 36 77.725 75.146 147.928 1.00162.86 S ATOM 8454 SG CYS E 39 80.413 77.076 147.426 1.00171.61 S Time building chain proxies: 12.21, per 1000 atoms: 0.57 Number of scatterers: 21526 At special positions: 0 Unit cell: (102.34, 131.58, 194.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 124 16.00 P 50 15.00 Mg 7 11.99 O 4172 8.00 N 3763 7.00 C 13409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 241 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.22 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 17 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 39 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 20 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 36 " Number of angles added : 6 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4782 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 18 sheets defined 30.1% alpha, 12.5% beta 5 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 9.26 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.645A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.515A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 366 through 373 removed outlier: 3.792A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.718A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASN B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'C' and resid 272 through 278 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.505A pdb=" N THR C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 366 through 374 Processing helix chain 'C' and resid 377 through 383 Processing helix chain 'C' and resid 406 through 414 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 438 through 456 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 372 through 375 No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 378 through 385 removed outlier: 3.856A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 Processing helix chain 'D' and resid 440 through 455 removed outlier: 3.666A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'E' and resid 88 through 94 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.513A pdb=" N CYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 247 through 255 removed outlier: 3.711A pdb=" N GLN E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 346 through 357 removed outlier: 3.724A pdb=" N ALA E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.717A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.606A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.972A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'F' and resid 88 through 94 Processing helix chain 'F' and resid 160 through 167 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 196 through 198 No H-bonds generated for 'chain 'F' and resid 196 through 198' Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'F' and resid 238 through 243 Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 295 through 298 No H-bonds generated for 'chain 'F' and resid 295 through 298' Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'F' and resid 346 through 357 removed outlier: 4.036A pdb=" N ALA F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 371 removed outlier: 3.805A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 385 removed outlier: 4.016A pdb=" N LEU F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 413 Processing helix chain 'F' and resid 440 through 456 Processing helix chain 'H' and resid 39 through 51 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.509A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 98 No H-bonds generated for 'chain 'H' and resid 95 through 98' Processing helix chain 'H' and resid 125 through 131 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 166 through 185 removed outlier: 3.830A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.575A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 246 removed outlier: 3.889A pdb=" N LEU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 377 through 399 removed outlier: 3.934A pdb=" N ALA H 381 " --> pdb=" O PRO H 377 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 408 No H-bonds generated for 'chain 'H' and resid 406 through 408' Processing helix chain 'H' and resid 449 through 452 No H-bonds generated for 'chain 'H' and resid 449 through 452' Processing helix chain 'H' and resid 479 through 487 removed outlier: 3.628A pdb=" N ALA H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 513 Processing helix chain 'H' and resid 518 through 529 removed outlier: 3.683A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 545 through 556 removed outlier: 4.028A pdb=" N LYS H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 573 Processing helix chain 'H' and resid 609 through 636 removed outlier: 4.088A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 683 removed outlier: 4.573A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 528 through 534 removed outlier: 7.008A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 542 through 544 removed outlier: 7.153A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 542 through 544 removed outlier: 6.964A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 498 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 528 through 533 removed outlier: 7.049A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU D 460 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL D 310 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 462 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 34 through 36 removed outlier: 3.742A pdb=" N ASN E 26 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR E 13 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 96 through 99 removed outlier: 3.527A pdb=" N VAL E 123 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E 131 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 175 through 177 removed outlier: 7.800A pdb=" N VAL E 176 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLN E 201 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL E 155 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE E 203 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 528 through 533 removed outlier: 7.013A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR E 498 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 502 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU E 460 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL E 310 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL E 462 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N SER E 312 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS E 464 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 97 through 100 removed outlier: 3.585A pdb=" N SER F 120 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.857A pdb=" N VAL F 154 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 176 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN F 201 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL F 155 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE F 203 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 528 through 533 removed outlier: 7.009A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 498 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU F 502 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU F 460 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL F 310 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL F 462 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.148A pdb=" N GLY H 21 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA H 7 " --> pdb=" O HIS H 19 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY H 21 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA H 5 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE H 23 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 3 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 56 through 58 Processing sheet with id= N, first strand: chain 'H' and resid 264 through 267 Processing sheet with id= O, first strand: chain 'H' and resid 419 through 421 Processing sheet with id= P, first strand: chain 'H' and resid 692 through 697 removed outlier: 3.618A pdb=" N ALA H 650 " --> pdb=" O GLN H 657 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY H 659 " --> pdb=" O TYR H 648 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR H 648 " --> pdb=" O GLY H 659 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 592 through 594 Processing sheet with id= R, first strand: chain 'H' and resid 574 through 579 removed outlier: 4.214A pdb=" N GLU H 575 " --> pdb=" O LYS H 587 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS H 587 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER H 577 " --> pdb=" O GLN H 585 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN H 585 " --> pdb=" O SER H 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 584 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 9.23 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: 3578 1.31 - 1.44: 5726 1.44 - 1.56: 12338 1.56 - 1.69: 91 1.69 - 1.82: 202 Bond restraints: 21935 Sorted by residual: bond pdb=" C4' DOC P 6 " pdb=" C3' DOC P 6 " ideal model delta sigma weight residual 1.334 1.517 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C4' DOC P 6 " pdb=" O4' DOC P 6 " ideal model delta sigma weight residual 1.609 1.440 0.169 2.00e-02 2.50e+03 7.11e+01 bond pdb=" O4' DOC P 6 " pdb=" C1' DOC P 6 " ideal model delta sigma weight residual 1.268 1.419 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C4 DOC P 6 " pdb=" N4 DOC P 6 " ideal model delta sigma weight residual 1.494 1.349 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C2 DOC P 6 " pdb=" N3 DOC P 6 " ideal model delta sigma weight residual 1.492 1.377 0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 21930 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.41: 607 106.41 - 113.41: 11957 113.41 - 120.42: 8716 120.42 - 127.43: 8176 127.43 - 134.43: 237 Bond angle restraints: 29693 Sorted by residual: angle pdb=" N GLN B 364 " pdb=" CA GLN B 364 " pdb=" C GLN B 364 " ideal model delta sigma weight residual 113.21 120.12 -6.91 1.15e+00 7.56e-01 3.61e+01 angle pdb=" C ARG B 363 " pdb=" CA ARG B 363 " pdb=" CB ARG B 363 " ideal model delta sigma weight residual 110.70 119.18 -8.48 1.83e+00 2.99e-01 2.15e+01 angle pdb=" PB TTP H 801 " pdb=" O3B TTP H 801 " pdb=" PG TTP H 801 " ideal model delta sigma weight residual 120.50 132.72 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" PA TTP H 801 " pdb=" O3A TTP H 801 " pdb=" PB TTP H 801 " ideal model delta sigma weight residual 120.50 132.69 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " pdb=" PB TTP C 700 " ideal model delta sigma weight residual 120.50 131.44 -10.94 3.00e+00 1.11e-01 1.33e+01 ... (remaining 29688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 12741 35.66 - 71.32: 216 71.32 - 106.99: 15 106.99 - 142.65: 3 142.65 - 178.31: 10 Dihedral angle restraints: 12985 sinusoidal: 5519 harmonic: 7466 Sorted by residual: dihedral pdb=" CD ARG H 604 " pdb=" NE ARG H 604 " pdb=" CZ ARG H 604 " pdb=" NH1 ARG H 604 " ideal model delta sinusoidal sigma weight residual 0.00 -73.24 73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CD ARG B 363 " pdb=" NE ARG B 363 " pdb=" CZ ARG B 363 " pdb=" NH1 ARG B 363 " ideal model delta sinusoidal sigma weight residual 0.00 67.33 -67.33 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" C5' TTP C 700 " pdb=" O5' TTP C 700 " pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " ideal model delta sinusoidal sigma weight residual 179.97 -1.72 -178.31 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 12982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2857 0.077 - 0.154: 406 0.154 - 0.231: 16 0.231 - 0.307: 10 0.307 - 0.384: 1 Chirality restraints: 3290 Sorted by residual: chirality pdb=" CA ILE E 261 " pdb=" N ILE E 261 " pdb=" C ILE E 261 " pdb=" CB ILE E 261 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" C3' TTP E 602 " pdb=" C2' TTP E 602 " pdb=" C4' TTP E 602 " pdb=" O3' TTP E 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' TTP F 700 " pdb=" C2' TTP F 700 " pdb=" C4' TTP F 700 " pdb=" O3' TTP F 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3287 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 604 " 1.052 9.50e-02 1.11e+02 4.72e-01 1.34e+02 pdb=" NE ARG H 604 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG H 604 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 604 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 604 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 363 " 1.011 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG B 363 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG B 363 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 363 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 363 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 229 " 0.387 9.50e-02 1.11e+02 1.74e-01 1.84e+01 pdb=" NE ARG F 229 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 229 " 0.013 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 310 2.68 - 3.23: 18045 3.23 - 3.79: 31355 3.79 - 4.34: 42027 4.34 - 4.90: 69431 Nonbonded interactions: 161168 Sorted by model distance: nonbonded pdb=" O2B TTP F 700 " pdb="MG MG F 701 " model vdw 2.125 2.170 nonbonded pdb=" O2G TTP D 700 " pdb="MG MG D 701 " model vdw 2.142 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.187 2.170 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 2.187 2.170 nonbonded pdb=" OG SER B 319 " pdb="MG MG B 701 " model vdw 2.197 2.170 ... (remaining 161163 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 264 through 395 or resid 405 through 430 or resid 439 or ( \ resid 440 and (name N or name CA or name C or name O or name CB )) or resid 441 \ through 546)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 342 or resid 346 thro \ ugh 363 or resid 370 through 395 or resid 405 through 430 or resid 439 or (resid \ 440 and (name N or name CA or name C or name O or name CB )) or resid 441 throu \ gh 505 or resid 511 through 546)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 342 or resid 346 thro \ ugh 363 or resid 370 through 395 or resid 405 through 430 or resid 439 or (resid \ 440 and (name N or name CA or name C or name O or name CB )) or resid 441 throu \ gh 505 or resid 511 through 546)) selection = (chain 'D' and (resid 264 through 342 or resid 346 through 363 or resid 370 thro \ ugh 395 or resid 405 through 430 or resid 439 through 505 or resid 511 through 5 \ 46)) } ncs_group { reference = (chain 'E' and (resid 65 through 292 or resid 294 through 545)) selection = (chain 'F' and (resid 65 through 208 or resid 219 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.220 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 68.220 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 21935 Z= 0.334 Angle : 0.824 12.221 29693 Z= 0.430 Chirality : 0.053 0.384 3290 Planarity : 0.013 0.472 3660 Dihedral : 13.899 178.309 8200 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 0.41 % Allowed : 3.58 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.13), residues: 2581 helix: -3.01 (0.11), residues: 896 sheet: -1.31 (0.24), residues: 451 loop : -3.00 (0.14), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 700 HIS 0.008 0.001 HIS C 425 PHE 0.024 0.002 PHE H 686 TYR 0.013 0.001 TYR H 648 ARG 0.006 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 651 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7700 (m-10) cc_final: 0.7380 (m-90) REVERT: A 361 ARG cc_start: 0.6894 (mmm-85) cc_final: 0.6518 (ttm110) REVERT: A 394 TYR cc_start: 0.8148 (t80) cc_final: 0.7886 (t80) REVERT: A 412 MET cc_start: 0.8187 (ttm) cc_final: 0.7766 (ttm) REVERT: A 443 ASP cc_start: 0.7981 (t0) cc_final: 0.7592 (t0) REVERT: A 515 LEU cc_start: 0.8919 (tt) cc_final: 0.8453 (mp) REVERT: B 352 ASP cc_start: 0.7800 (m-30) cc_final: 0.7336 (m-30) REVERT: B 375 ASN cc_start: 0.8788 (p0) cc_final: 0.8180 (p0) REVERT: B 437 ASP cc_start: 0.7747 (t70) cc_final: 0.7303 (p0) REVERT: B 497 ASP cc_start: 0.8896 (m-30) cc_final: 0.8119 (t0) REVERT: C 300 LEU cc_start: 0.8993 (mt) cc_final: 0.8755 (tt) REVERT: C 316 MET cc_start: 0.9048 (mmm) cc_final: 0.8846 (mmm) REVERT: C 494 GLN cc_start: 0.8997 (mt0) cc_final: 0.8685 (mt0) REVERT: D 316 MET cc_start: 0.9055 (mmp) cc_final: 0.8473 (mmm) REVERT: D 370 ARG cc_start: 0.8404 (ptp-170) cc_final: 0.8191 (ttp-110) REVERT: D 405 LEU cc_start: 0.9035 (tp) cc_final: 0.8763 (tt) REVERT: D 409 LEU cc_start: 0.9672 (mt) cc_final: 0.9448 (mt) REVERT: D 456 THR cc_start: 0.8565 (p) cc_final: 0.7990 (p) REVERT: E 187 LYS cc_start: 0.9418 (tppt) cc_final: 0.9088 (ttpt) REVERT: E 251 MET cc_start: 0.8332 (mmm) cc_final: 0.7957 (mmt) REVERT: E 255 TRP cc_start: 0.8609 (m100) cc_final: 0.8088 (m100) REVERT: E 256 ASN cc_start: 0.8300 (m110) cc_final: 0.7891 (t0) REVERT: E 303 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6643 (mtt-85) REVERT: E 370 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.7835 (tmm-80) REVERT: E 497 ASP cc_start: 0.8258 (m-30) cc_final: 0.7990 (t0) REVERT: F 91 CYS cc_start: 0.8710 (m) cc_final: 0.8386 (p) REVERT: F 142 PHE cc_start: 0.6956 (t80) cc_final: 0.6660 (t80) REVERT: F 163 LEU cc_start: 0.9005 (mt) cc_final: 0.8800 (mt) REVERT: F 166 MET cc_start: 0.8699 (mtp) cc_final: 0.8390 (mtp) REVERT: F 359 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6810 (mmp80) REVERT: F 412 MET cc_start: 0.8870 (mtt) cc_final: 0.8650 (mtm) REVERT: F 425 HIS cc_start: 0.7202 (t-90) cc_final: 0.6511 (t-170) REVERT: F 526 ASP cc_start: 0.8834 (p0) cc_final: 0.8451 (p0) REVERT: H 130 TYR cc_start: 0.8383 (m-80) cc_final: 0.8167 (m-80) REVERT: H 179 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7593 (pttp) REVERT: H 332 VAL cc_start: 0.8824 (p) cc_final: 0.8420 (m) REVERT: H 585 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6567 (tt0) REVERT: H 630 GLU cc_start: 0.7993 (pt0) cc_final: 0.7745 (pm20) REVERT: H 677 MET cc_start: 0.8281 (tpt) cc_final: 0.7833 (tpt) outliers start: 9 outliers final: 1 residues processed: 657 average time/residue: 0.4013 time to fit residues: 376.1940 Evaluate side-chains 301 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 303 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 0.3980 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 239 optimal weight: 0.6980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS B 296 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN C 475 HIS C 536 ASN D 358 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN E 70 ASN E 129 ASN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN E 253 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN E 444 ASN E 494 GLN E 512 ASN F 107 GLN F 136 HIS ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN H 62 HIS H 230 ASN H 331 HIS H 423 ASN H 439 GLN H 520 ASN H 558 ASN H 607 HIS H 640 HIS H 685 ASN H 704 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21935 Z= 0.262 Angle : 0.599 10.021 29693 Z= 0.305 Chirality : 0.044 0.187 3290 Planarity : 0.004 0.078 3660 Dihedral : 14.881 178.427 3271 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.72 % Allowed : 10.73 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.72 (0.15), residues: 2581 helix: -1.25 (0.16), residues: 909 sheet: -1.01 (0.24), residues: 461 loop : -2.57 (0.15), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 351 HIS 0.008 0.001 HIS B 465 PHE 0.023 0.002 PHE H 234 TYR 0.013 0.001 TYR E 535 ARG 0.006 0.001 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 300 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7955 (m-10) cc_final: 0.7421 (m-90) REVERT: A 351 GLU cc_start: 0.8826 (pt0) cc_final: 0.8549 (pp20) REVERT: A 361 ARG cc_start: 0.7149 (mmm-85) cc_final: 0.6468 (ttm110) REVERT: A 394 TYR cc_start: 0.8150 (t80) cc_final: 0.7884 (t80) REVERT: A 440 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8488 (ttmm) REVERT: B 348 GLU cc_start: 0.7606 (mp0) cc_final: 0.7205 (mp0) REVERT: B 352 ASP cc_start: 0.7866 (m-30) cc_final: 0.7367 (m-30) REVERT: B 437 ASP cc_start: 0.7923 (t70) cc_final: 0.7462 (p0) REVERT: B 497 ASP cc_start: 0.9053 (m-30) cc_final: 0.8064 (t0) REVERT: C 341 MET cc_start: 0.9114 (mmt) cc_final: 0.8905 (mmt) REVERT: D 316 MET cc_start: 0.9107 (mmp) cc_final: 0.8573 (mmm) REVERT: D 370 ARG cc_start: 0.8434 (ptp-170) cc_final: 0.8203 (mtm110) REVERT: D 380 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7936 (tm-30) REVERT: E 187 LYS cc_start: 0.9413 (tppt) cc_final: 0.9152 (ttpt) REVERT: E 256 ASN cc_start: 0.8421 (m110) cc_final: 0.8203 (t0) REVERT: E 306 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6863 (mm-30) REVERT: E 314 SER cc_start: 0.9456 (m) cc_final: 0.9230 (t) REVERT: E 370 ARG cc_start: 0.8289 (ptp-170) cc_final: 0.7915 (tmm-80) REVERT: F 91 CYS cc_start: 0.8621 (m) cc_final: 0.8195 (p) REVERT: F 131 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7192 (mtpp) REVERT: F 137 LYS cc_start: 0.6634 (pttm) cc_final: 0.6427 (pttm) REVERT: F 142 PHE cc_start: 0.7441 (t80) cc_final: 0.6816 (t80) REVERT: F 166 MET cc_start: 0.8649 (mtp) cc_final: 0.8414 (mtp) REVERT: F 217 GLU cc_start: 0.8573 (tp30) cc_final: 0.8200 (mt-10) REVERT: F 309 MET cc_start: 0.7576 (tpp) cc_final: 0.7138 (mtt) REVERT: F 359 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7253 (mtp85) REVERT: F 412 MET cc_start: 0.8983 (mtt) cc_final: 0.8646 (mtm) REVERT: H 17 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8084 (mppt) REVERT: H 179 LYS cc_start: 0.8086 (tmtt) cc_final: 0.7579 (pttp) REVERT: H 378 GLU cc_start: 0.8127 (mp0) cc_final: 0.7879 (mp0) REVERT: H 461 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8534 (pp) REVERT: H 585 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6610 (tt0) REVERT: H 677 MET cc_start: 0.8537 (tpt) cc_final: 0.8195 (tpt) outliers start: 60 outliers final: 47 residues processed: 345 average time/residue: 0.3547 time to fit residues: 183.5404 Evaluate side-chains 305 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 256 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 607 HIS Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 380 GLN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 HIS H 607 HIS H 640 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21935 Z= 0.322 Angle : 0.606 9.499 29693 Z= 0.307 Chirality : 0.044 0.162 3290 Planarity : 0.004 0.065 3660 Dihedral : 14.865 179.789 3267 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.62 % Allowed : 12.05 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.14 (0.16), residues: 2581 helix: -0.49 (0.17), residues: 907 sheet: -0.91 (0.24), residues: 460 loop : -2.36 (0.15), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 69 HIS 0.007 0.001 HIS C 465 PHE 0.021 0.002 PHE C 523 TYR 0.017 0.001 TYR C 411 ARG 0.011 0.001 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 267 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8021 (m-10) cc_final: 0.7458 (m-90) REVERT: A 351 GLU cc_start: 0.8801 (pt0) cc_final: 0.8581 (pp20) REVERT: A 394 TYR cc_start: 0.8154 (t80) cc_final: 0.7932 (t80) REVERT: A 440 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8477 (ttmm) REVERT: B 352 ASP cc_start: 0.8054 (m-30) cc_final: 0.7520 (m-30) REVERT: B 437 ASP cc_start: 0.7852 (t70) cc_final: 0.7421 (p0) REVERT: B 526 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: B 542 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8945 (pp) REVERT: D 316 MET cc_start: 0.9138 (mmp) cc_final: 0.8606 (mmm) REVERT: D 370 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8233 (mtm110) REVERT: D 380 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 499 ILE cc_start: 0.9282 (mp) cc_final: 0.8956 (mm) REVERT: E 147 TRP cc_start: 0.7560 (m-10) cc_final: 0.7262 (m-10) REVERT: E 170 ASP cc_start: 0.8562 (t0) cc_final: 0.8252 (t0) REVERT: E 172 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8279 (mtmm) REVERT: E 187 LYS cc_start: 0.9451 (tppt) cc_final: 0.9195 (ttpt) REVERT: E 256 ASN cc_start: 0.8515 (m110) cc_final: 0.8158 (t0) REVERT: E 370 ARG cc_start: 0.8296 (ptp-170) cc_final: 0.7956 (tmm-80) REVERT: F 88 LYS cc_start: 0.6791 (pptt) cc_final: 0.6367 (tttm) REVERT: F 91 CYS cc_start: 0.8629 (m) cc_final: 0.8297 (m) REVERT: F 131 LYS cc_start: 0.7459 (ttpp) cc_final: 0.7024 (mtpp) REVERT: F 137 LYS cc_start: 0.6658 (pttm) cc_final: 0.6448 (pttm) REVERT: F 142 PHE cc_start: 0.7633 (t80) cc_final: 0.6900 (t80) REVERT: F 162 MET cc_start: 0.8323 (tmm) cc_final: 0.7754 (tmm) REVERT: F 166 MET cc_start: 0.8623 (mtp) cc_final: 0.8350 (mtp) REVERT: F 169 GLN cc_start: 0.8110 (mt0) cc_final: 0.7895 (pt0) REVERT: F 309 MET cc_start: 0.7584 (tpp) cc_final: 0.7200 (mtt) REVERT: F 359 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7413 (mtp85) REVERT: F 425 HIS cc_start: 0.7942 (t-90) cc_final: 0.7494 (t-90) REVERT: F 526 ASP cc_start: 0.8927 (p0) cc_final: 0.8653 (p0) REVERT: H 17 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8087 (mppt) REVERT: H 179 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7506 (pttp) REVERT: H 359 LYS cc_start: 0.7890 (pmmt) cc_final: 0.7595 (mmtt) REVERT: H 378 GLU cc_start: 0.8141 (mp0) cc_final: 0.7887 (mp0) REVERT: H 585 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6720 (tt0) REVERT: H 614 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7391 (mt) REVERT: H 630 GLU cc_start: 0.8178 (pt0) cc_final: 0.7915 (pp20) REVERT: H 677 MET cc_start: 0.8575 (tpt) cc_final: 0.8300 (tpt) outliers start: 80 outliers final: 58 residues processed: 327 average time/residue: 0.3448 time to fit residues: 171.1762 Evaluate side-chains 304 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 607 HIS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21935 Z= 0.209 Angle : 0.545 9.660 29693 Z= 0.273 Chirality : 0.042 0.146 3290 Planarity : 0.003 0.062 3660 Dihedral : 14.602 179.447 3267 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.85 % Allowed : 13.77 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.75 (0.16), residues: 2581 helix: -0.06 (0.18), residues: 908 sheet: -0.77 (0.24), residues: 469 loop : -2.21 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 97 HIS 0.005 0.001 HIS C 465 PHE 0.018 0.001 PHE F 452 TYR 0.015 0.001 TYR C 411 ARG 0.010 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 258 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7942 (m-10) cc_final: 0.7435 (m-90) REVERT: A 351 GLU cc_start: 0.8854 (pt0) cc_final: 0.8610 (pp20) REVERT: B 333 MET cc_start: 0.8693 (mpp) cc_final: 0.8427 (mpp) REVERT: B 348 GLU cc_start: 0.7784 (mp0) cc_final: 0.7415 (mp0) REVERT: B 352 ASP cc_start: 0.8091 (m-30) cc_final: 0.7562 (m-30) REVERT: B 437 ASP cc_start: 0.7813 (t70) cc_final: 0.7309 (p0) REVERT: B 497 ASP cc_start: 0.9010 (m-30) cc_final: 0.8617 (m-30) REVERT: B 526 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: B 533 MET cc_start: 0.7945 (mtm) cc_final: 0.7562 (mtm) REVERT: B 542 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8972 (pp) REVERT: D 316 MET cc_start: 0.9110 (mmp) cc_final: 0.8561 (mmm) REVERT: D 370 ARG cc_start: 0.8502 (ptp-170) cc_final: 0.8239 (mtm110) REVERT: D 380 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7932 (tm-30) REVERT: D 499 ILE cc_start: 0.9260 (mp) cc_final: 0.8948 (mm) REVERT: E 147 TRP cc_start: 0.7713 (m-10) cc_final: 0.7497 (m-10) REVERT: E 170 ASP cc_start: 0.8604 (t0) cc_final: 0.8385 (t0) REVERT: E 187 LYS cc_start: 0.9478 (tppt) cc_final: 0.9214 (ttpt) REVERT: E 256 ASN cc_start: 0.8527 (m110) cc_final: 0.8144 (t0) REVERT: E 260 TRP cc_start: 0.8407 (p-90) cc_final: 0.7981 (p-90) REVERT: E 306 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 370 ARG cc_start: 0.8259 (ptp-170) cc_final: 0.7942 (tmm-80) REVERT: F 91 CYS cc_start: 0.8660 (m) cc_final: 0.8223 (p) REVERT: F 131 LYS cc_start: 0.7140 (ttpp) cc_final: 0.6881 (mtpt) REVERT: F 137 LYS cc_start: 0.6711 (pttm) cc_final: 0.6468 (pttm) REVERT: F 142 PHE cc_start: 0.7658 (t80) cc_final: 0.7010 (t80) REVERT: F 166 MET cc_start: 0.8624 (mtp) cc_final: 0.8384 (mtp) REVERT: F 169 GLN cc_start: 0.8146 (mt0) cc_final: 0.7857 (pt0) REVERT: F 359 ARG cc_start: 0.7716 (mmt-90) cc_final: 0.7407 (mtp85) REVERT: F 425 HIS cc_start: 0.7939 (t-90) cc_final: 0.7492 (t-90) REVERT: F 526 ASP cc_start: 0.8924 (p0) cc_final: 0.8679 (p0) REVERT: H 17 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8200 (mppt) REVERT: H 167 MET cc_start: 0.7060 (ttm) cc_final: 0.6826 (mtp) REVERT: H 223 LEU cc_start: 0.8279 (tp) cc_final: 0.7855 (tp) REVERT: H 359 LYS cc_start: 0.7911 (pmmt) cc_final: 0.7571 (mmtt) REVERT: H 378 GLU cc_start: 0.8193 (mp0) cc_final: 0.7902 (mp0) REVERT: H 585 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6754 (tt0) REVERT: H 630 GLU cc_start: 0.8183 (pt0) cc_final: 0.7896 (pt0) outliers start: 63 outliers final: 48 residues processed: 303 average time/residue: 0.3575 time to fit residues: 167.7529 Evaluate side-chains 290 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 607 HIS Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 0.0060 chunk 64 optimal weight: 4.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21935 Z= 0.311 Angle : 0.593 7.568 29693 Z= 0.301 Chirality : 0.044 0.192 3290 Planarity : 0.004 0.060 3660 Dihedral : 14.641 175.564 3267 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.94 % Allowed : 13.54 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.53 (0.16), residues: 2581 helix: 0.17 (0.18), residues: 916 sheet: -0.66 (0.25), residues: 452 loop : -2.13 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 97 HIS 0.006 0.001 HIS C 465 PHE 0.015 0.002 PHE C 523 TYR 0.019 0.001 TYR A 394 ARG 0.007 0.001 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 237 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8178 (m-10) cc_final: 0.7579 (m-90) REVERT: A 351 GLU cc_start: 0.8954 (pt0) cc_final: 0.8633 (pp20) REVERT: B 348 GLU cc_start: 0.7895 (mp0) cc_final: 0.7363 (mp0) REVERT: B 352 ASP cc_start: 0.8135 (m-30) cc_final: 0.7484 (m-30) REVERT: B 437 ASP cc_start: 0.7773 (t70) cc_final: 0.7365 (p0) REVERT: B 497 ASP cc_start: 0.8935 (m-30) cc_final: 0.8509 (m-30) REVERT: B 526 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: D 306 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: D 316 MET cc_start: 0.9077 (mmp) cc_final: 0.8577 (mmm) REVERT: D 370 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.8269 (mtm110) REVERT: D 380 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7985 (tm-30) REVERT: E 187 LYS cc_start: 0.9537 (tppt) cc_final: 0.9268 (ttpt) REVERT: E 256 ASN cc_start: 0.8580 (m110) cc_final: 0.8074 (t0) REVERT: E 260 TRP cc_start: 0.8381 (p-90) cc_final: 0.7828 (p-90) REVERT: E 306 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 404 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5278 (pmt-80) REVERT: F 91 CYS cc_start: 0.8695 (m) cc_final: 0.8274 (p) REVERT: F 137 LYS cc_start: 0.6640 (pttm) cc_final: 0.6124 (pttm) REVERT: F 142 PHE cc_start: 0.7847 (t80) cc_final: 0.7207 (t80) REVERT: F 169 GLN cc_start: 0.8178 (mt0) cc_final: 0.7878 (pt0) REVERT: F 359 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7579 (mtp85) REVERT: F 412 MET cc_start: 0.8822 (mtp) cc_final: 0.8318 (mtm) REVERT: H 17 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8269 (mppt) REVERT: H 359 LYS cc_start: 0.7820 (pmmt) cc_final: 0.7544 (mmtt) REVERT: H 514 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4843 (pp20) REVERT: H 585 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6751 (tt0) REVERT: H 630 GLU cc_start: 0.8225 (pt0) cc_final: 0.7897 (pp20) outliers start: 87 outliers final: 68 residues processed: 304 average time/residue: 0.3769 time to fit residues: 175.7224 Evaluate side-chains 293 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 220 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 380 GLN Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 189 LYS Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21935 Z= 0.236 Angle : 0.549 9.152 29693 Z= 0.278 Chirality : 0.043 0.242 3290 Planarity : 0.003 0.064 3660 Dihedral : 14.461 175.027 3267 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.71 % Allowed : 14.49 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.32 (0.17), residues: 2581 helix: 0.39 (0.18), residues: 915 sheet: -0.58 (0.25), residues: 468 loop : -2.05 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 147 HIS 0.005 0.001 HIS C 425 PHE 0.016 0.001 PHE E 452 TYR 0.015 0.001 TYR A 394 ARG 0.015 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 235 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8132 (m-10) cc_final: 0.7551 (m-90) REVERT: A 351 GLU cc_start: 0.8944 (pt0) cc_final: 0.8680 (pp20) REVERT: B 437 ASP cc_start: 0.7746 (t70) cc_final: 0.7285 (p0) REVERT: B 497 ASP cc_start: 0.8902 (m-30) cc_final: 0.8550 (m-30) REVERT: B 526 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: D 306 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: D 316 MET cc_start: 0.9021 (mmp) cc_final: 0.8546 (mmm) REVERT: D 370 ARG cc_start: 0.8492 (ptp-170) cc_final: 0.8275 (mtm110) REVERT: D 380 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7968 (tm-30) REVERT: E 41 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7502 (ptpp) REVERT: E 187 LYS cc_start: 0.9538 (tppt) cc_final: 0.9278 (ttpt) REVERT: E 256 ASN cc_start: 0.8562 (m110) cc_final: 0.8043 (t0) REVERT: E 260 TRP cc_start: 0.8271 (p-90) cc_final: 0.7794 (p-90) REVERT: E 306 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7836 (mm-30) REVERT: E 404 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.4625 (pmt-80) REVERT: F 77 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8190 (mmp80) REVERT: F 91 CYS cc_start: 0.8713 (m) cc_final: 0.8257 (p) REVERT: F 130 PHE cc_start: 0.5356 (t80) cc_final: 0.5134 (t80) REVERT: F 137 LYS cc_start: 0.6639 (pttm) cc_final: 0.6076 (pttm) REVERT: F 142 PHE cc_start: 0.7584 (t80) cc_final: 0.7093 (t80) REVERT: F 169 GLN cc_start: 0.8199 (mt0) cc_final: 0.7923 (pt0) REVERT: F 359 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7578 (mtp85) REVERT: H 17 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8390 (mppt) REVERT: H 359 LYS cc_start: 0.7790 (pmmt) cc_final: 0.7514 (mmtt) REVERT: H 514 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.4928 (pp20) REVERT: H 585 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6799 (tt0) outliers start: 82 outliers final: 58 residues processed: 301 average time/residue: 0.3473 time to fit residues: 160.6047 Evaluate side-chains 281 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 217 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 189 LYS Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 155 optimal weight: 0.2980 chunk 117 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21935 Z= 0.197 Angle : 0.535 10.610 29693 Z= 0.271 Chirality : 0.042 0.176 3290 Planarity : 0.003 0.056 3660 Dihedral : 14.342 173.208 3267 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.71 % Allowed : 15.26 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.15 (0.17), residues: 2581 helix: 0.53 (0.18), residues: 914 sheet: -0.50 (0.25), residues: 468 loop : -1.94 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP E 147 HIS 0.005 0.001 HIS C 425 PHE 0.019 0.001 PHE F 142 TYR 0.014 0.001 TYR A 394 ARG 0.010 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 226 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8121 (m-10) cc_final: 0.7519 (m-90) REVERT: A 351 GLU cc_start: 0.8935 (pt0) cc_final: 0.8664 (pp20) REVERT: B 437 ASP cc_start: 0.7688 (t70) cc_final: 0.7263 (p0) REVERT: B 497 ASP cc_start: 0.8877 (m-30) cc_final: 0.8529 (m-30) REVERT: B 526 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: D 306 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: D 316 MET cc_start: 0.8996 (mmp) cc_final: 0.8525 (mmm) REVERT: D 370 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8284 (mtm110) REVERT: D 380 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7953 (tm-30) REVERT: E 41 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7524 (ptpp) REVERT: E 187 LYS cc_start: 0.9544 (tppt) cc_final: 0.9278 (ttpt) REVERT: E 256 ASN cc_start: 0.8554 (m110) cc_final: 0.8035 (t0) REVERT: E 260 TRP cc_start: 0.8209 (p-90) cc_final: 0.7704 (p-90) REVERT: E 306 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7837 (mm-30) REVERT: E 404 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.4684 (pmt-80) REVERT: F 91 CYS cc_start: 0.8710 (m) cc_final: 0.8255 (p) REVERT: F 97 TRP cc_start: 0.8045 (p-90) cc_final: 0.7626 (p-90) REVERT: F 137 LYS cc_start: 0.6600 (pttm) cc_final: 0.6294 (pttm) REVERT: F 142 PHE cc_start: 0.7558 (t80) cc_final: 0.7305 (t80) REVERT: F 169 GLN cc_start: 0.8281 (mt0) cc_final: 0.7941 (pt0) REVERT: F 359 ARG cc_start: 0.7893 (mmt-90) cc_final: 0.7555 (mtp85) REVERT: H 183 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8494 (mm-30) REVERT: H 359 LYS cc_start: 0.7816 (pmmt) cc_final: 0.7535 (mmtt) REVERT: H 514 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4938 (pp20) REVERT: H 585 GLN cc_start: 0.7317 (mm-40) cc_final: 0.6801 (tt0) outliers start: 82 outliers final: 66 residues processed: 291 average time/residue: 0.3330 time to fit residues: 149.2090 Evaluate side-chains 288 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 217 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 189 LYS Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 640 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21935 Z= 0.377 Angle : 0.659 10.734 29693 Z= 0.333 Chirality : 0.045 0.146 3290 Planarity : 0.004 0.073 3660 Dihedral : 14.563 174.111 3267 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.89 % Allowed : 15.31 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2581 helix: 0.38 (0.18), residues: 919 sheet: -0.59 (0.26), residues: 449 loop : -1.99 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 147 HIS 0.008 0.001 HIS C 425 PHE 0.018 0.002 PHE F 142 TYR 0.014 0.001 TYR A 394 ARG 0.015 0.001 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 215 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8195 (m-10) cc_final: 0.7561 (m-90) REVERT: A 351 GLU cc_start: 0.8998 (pt0) cc_final: 0.8694 (pp20) REVERT: B 437 ASP cc_start: 0.7817 (t70) cc_final: 0.7338 (p0) REVERT: B 526 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: D 306 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: D 316 MET cc_start: 0.9000 (mmp) cc_final: 0.8563 (mmm) REVERT: D 370 ARG cc_start: 0.8580 (ptp-170) cc_final: 0.8301 (mtm110) REVERT: D 380 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7900 (tm-30) REVERT: E 19 ASN cc_start: 0.9065 (t0) cc_final: 0.8529 (m-40) REVERT: E 187 LYS cc_start: 0.9559 (tppt) cc_final: 0.9299 (ttpt) REVERT: E 260 TRP cc_start: 0.8276 (p-90) cc_final: 0.7631 (p-90) REVERT: E 306 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7940 (mm-30) REVERT: E 352 ASP cc_start: 0.8131 (t0) cc_final: 0.7929 (t0) REVERT: E 404 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5443 (pmt-80) REVERT: F 77 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8131 (mmp80) REVERT: F 91 CYS cc_start: 0.8775 (m) cc_final: 0.8328 (p) REVERT: F 137 LYS cc_start: 0.6326 (pttm) cc_final: 0.6076 (pttm) REVERT: F 309 MET cc_start: 0.7321 (ttm) cc_final: 0.7047 (mtt) REVERT: F 359 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7656 (mtp85) REVERT: H 183 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8463 (mm-30) REVERT: H 359 LYS cc_start: 0.7899 (pmmt) cc_final: 0.7616 (mmtt) REVERT: H 514 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4982 (pp20) REVERT: H 585 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6772 (pt0) REVERT: H 630 GLU cc_start: 0.8242 (tt0) cc_final: 0.7888 (pt0) outliers start: 86 outliers final: 74 residues processed: 284 average time/residue: 0.3324 time to fit residues: 144.8971 Evaluate side-chains 283 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 205 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 341 MET Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 189 LYS Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 0.0030 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 0.1980 chunk 155 optimal weight: 0.3980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21935 Z= 0.156 Angle : 0.540 10.986 29693 Z= 0.272 Chirality : 0.042 0.158 3290 Planarity : 0.003 0.064 3660 Dihedral : 14.287 175.429 3267 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.40 % Allowed : 16.85 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.02 (0.17), residues: 2581 helix: 0.63 (0.18), residues: 916 sheet: -0.50 (0.25), residues: 471 loop : -1.81 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP E 147 HIS 0.006 0.001 HIS C 425 PHE 0.036 0.001 PHE F 142 TYR 0.013 0.001 TYR A 394 ARG 0.014 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8092 (m-10) cc_final: 0.7500 (m-90) REVERT: A 351 GLU cc_start: 0.8941 (pt0) cc_final: 0.8662 (pp20) REVERT: B 437 ASP cc_start: 0.7735 (t70) cc_final: 0.7217 (p0) REVERT: D 316 MET cc_start: 0.8907 (mmp) cc_final: 0.8471 (mmm) REVERT: D 370 ARG cc_start: 0.8574 (ptp-170) cc_final: 0.8296 (mtm110) REVERT: D 380 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7949 (tm-30) REVERT: E 157 GLU cc_start: 0.7372 (pt0) cc_final: 0.6756 (pm20) REVERT: E 187 LYS cc_start: 0.9561 (tppt) cc_final: 0.9308 (ttpt) REVERT: E 256 ASN cc_start: 0.8517 (m110) cc_final: 0.7968 (t0) REVERT: E 260 TRP cc_start: 0.8194 (p-90) cc_final: 0.7714 (p-90) REVERT: E 306 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7898 (mm-30) REVERT: F 91 CYS cc_start: 0.8785 (m) cc_final: 0.8298 (p) REVERT: F 97 TRP cc_start: 0.8040 (p-90) cc_final: 0.7570 (p-90) REVERT: F 137 LYS cc_start: 0.6565 (pttm) cc_final: 0.6027 (pttm) REVERT: F 359 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7529 (mtp85) REVERT: H 183 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8477 (mm-30) REVERT: H 359 LYS cc_start: 0.7798 (pmmt) cc_final: 0.7574 (mmtt) REVERT: H 391 MET cc_start: 0.7877 (tmm) cc_final: 0.7277 (tmm) REVERT: H 514 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.4941 (pp20) REVERT: H 585 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6722 (pt0) REVERT: H 630 GLU cc_start: 0.8102 (tt0) cc_final: 0.7805 (pp20) outliers start: 53 outliers final: 42 residues processed: 259 average time/residue: 0.3415 time to fit residues: 135.2356 Evaluate side-chains 251 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 208 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 0.0670 chunk 174 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 161 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 overall best weight: 3.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21935 Z= 0.362 Angle : 0.648 11.707 29693 Z= 0.326 Chirality : 0.045 0.171 3290 Planarity : 0.004 0.065 3660 Dihedral : 14.384 175.187 3267 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.54 % Allowed : 16.85 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.12 (0.17), residues: 2581 helix: 0.54 (0.18), residues: 919 sheet: -0.56 (0.25), residues: 460 loop : -1.87 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 147 HIS 0.009 0.001 HIS C 425 PHE 0.016 0.002 PHE F 71 TYR 0.013 0.001 TYR A 394 ARG 0.014 0.001 ARG F 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 209 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8171 (m-10) cc_final: 0.7532 (m-90) REVERT: A 351 GLU cc_start: 0.8991 (pt0) cc_final: 0.8701 (pp20) REVERT: D 316 MET cc_start: 0.8969 (mmp) cc_final: 0.8589 (mmm) REVERT: D 370 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.8352 (mtm110) REVERT: D 380 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7888 (tm-30) REVERT: E 19 ASN cc_start: 0.9061 (t0) cc_final: 0.8501 (m-40) REVERT: E 187 LYS cc_start: 0.9578 (tppt) cc_final: 0.9315 (ttpt) REVERT: E 260 TRP cc_start: 0.8203 (p-90) cc_final: 0.7703 (p-90) REVERT: E 352 ASP cc_start: 0.8165 (t0) cc_final: 0.7964 (t0) REVERT: F 91 CYS cc_start: 0.8806 (m) cc_final: 0.8333 (p) REVERT: F 97 TRP cc_start: 0.7983 (p-90) cc_final: 0.7499 (p-90) REVERT: F 137 LYS cc_start: 0.6259 (pttm) cc_final: 0.5857 (pttm) REVERT: F 309 MET cc_start: 0.7313 (ttm) cc_final: 0.7029 (mtt) REVERT: F 359 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7665 (mtp85) REVERT: H 183 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8473 (mm-30) REVERT: H 359 LYS cc_start: 0.7842 (pmmt) cc_final: 0.7566 (mmtt) REVERT: H 514 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.5041 (pp20) REVERT: H 585 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6787 (pt0) outliers start: 56 outliers final: 51 residues processed: 253 average time/residue: 0.3373 time to fit residues: 131.3573 Evaluate side-chains 258 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 189 LYS Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.078445 restraints weight = 43583.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.079538 restraints weight = 28213.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080202 restraints weight = 19115.239| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21935 Z= 0.228 Angle : 0.578 11.789 29693 Z= 0.290 Chirality : 0.043 0.147 3290 Planarity : 0.003 0.059 3660 Dihedral : 14.241 168.727 3267 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.40 % Allowed : 17.07 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.02 (0.17), residues: 2581 helix: 0.62 (0.18), residues: 920 sheet: -0.54 (0.25), residues: 466 loop : -1.79 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 42 HIS 0.007 0.001 HIS C 425 PHE 0.019 0.001 PHE E 71 TYR 0.012 0.001 TYR A 394 ARG 0.013 0.000 ARG F 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4366.76 seconds wall clock time: 79 minutes 36.66 seconds (4776.66 seconds total)