Starting phenix.real_space_refine on Thu May 15 00:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7r_18230/05_2025/8q7r_18230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7r_18230/05_2025/8q7r_18230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7r_18230/05_2025/8q7r_18230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7r_18230/05_2025/8q7r_18230.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7r_18230/05_2025/8q7r_18230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7r_18230/05_2025/8q7r_18230.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 80 5.16 5 C 7996 2.51 5 N 2162 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12536 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4582 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 17, 'TRANS': 604} Chain breaks: 4 Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 34, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 349 Chain: "H" Number of atoms: 4328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4328 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 570} Chain breaks: 6 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 153 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 40 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1047 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 13, 'TRANS': 148} Chain breaks: 4 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 162, 1047 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 13, 'TRANS': 148} Chain breaks: 4 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 1063 Chain: "D" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 671 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 729 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 91} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 548 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'U9O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12134 SG CYS R 42 49.223 72.893 56.598 1.00 68.29 S ATOM 12150 SG CYS R 45 48.339 69.492 58.509 1.00 65.56 S ATOM 12360 SG CYS R 83 48.083 72.779 60.264 1.00 73.17 S ATOM 12289 SG CYS R 75 51.831 86.414 50.724 1.00 84.04 S ATOM 12445 SG CYS R 94 51.858 84.349 54.082 1.00 73.92 S ATOM 12200 SG CYS R 53 42.888 70.402 60.615 1.00 77.11 S ATOM 12219 SG CYS R 56 40.368 69.087 63.141 1.00 78.49 S ATOM 12245 SG CYS R 68 39.414 71.845 60.483 1.00 71.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 138 " occ=0.59 ... (10 atoms not shown) pdb=" OG BSER C 138 " occ=0.41 Time building chain proxies: 8.50, per 1000 atoms: 0.68 Number of scatterers: 12536 At special positions: 0 Unit cell: (132.787, 148.96, 171.091, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 80 16.00 O 2295 8.00 N 2162 7.00 C 7996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N U9O U 701 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " Number of angles added : 6 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 20 sheets defined 52.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 removed outlier: 3.737A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.692A pdb=" N VAL A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 21 through 25' Processing helix chain 'A' and resid 33 through 46 removed outlier: 3.873A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.969A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 228 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 235 through 251 removed outlier: 3.926A pdb=" N GLU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 291 through 303 removed outlier: 5.187A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.512A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.670A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 410 through 424 removed outlier: 4.574A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.967A pdb=" N LYS A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 470 through 496 removed outlier: 3.802A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.919A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 596 through 603 removed outlier: 4.199A pdb=" N THR A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 119 through 132 removed outlier: 4.235A pdb=" N ILE C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 159 through 179 Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.138A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 Processing helix chain 'D' and resid 67 through 83 removed outlier: 4.086A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 5.738A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 34 removed outlier: 3.921A pdb=" N ARG G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing helix chain 'H' and resid 251 through 259 removed outlier: 3.534A pdb=" N VAL H 256 " --> pdb=" O GLY H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 267 Processing helix chain 'H' and resid 305 through 308 Processing helix chain 'H' and resid 315 through 330 Processing helix chain 'H' and resid 335 through 351 Processing helix chain 'H' and resid 355 through 371 removed outlier: 3.838A pdb=" N ASN H 359 " --> pdb=" O LYS H 355 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP H 361 " --> pdb=" O CYS H 357 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS H 362 " --> pdb=" O ILE H 358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR H 363 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 364 " --> pdb=" O LEU H 360 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER H 370 " --> pdb=" O ASP H 366 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN H 371 " --> pdb=" O MET H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 394 removed outlier: 4.147A pdb=" N SER H 381 " --> pdb=" O PRO H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 427 removed outlier: 3.670A pdb=" N GLU H 421 " --> pdb=" O LYS H 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE H 422 " --> pdb=" O SER H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 454 removed outlier: 4.098A pdb=" N LYS H 454 " --> pdb=" O CYS H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 475 removed outlier: 4.385A pdb=" N HIS H 463 " --> pdb=" O LEU H 459 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE H 464 " --> pdb=" O GLU H 460 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 475 " --> pdb=" O ARG H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 490 Processing helix chain 'H' and resid 492 through 495 No H-bonds generated for 'chain 'H' and resid 492 through 495' Processing helix chain 'H' and resid 508 through 517 removed outlier: 3.604A pdb=" N LEU H 514 " --> pdb=" O VAL H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 538 removed outlier: 3.725A pdb=" N ASN H 538 " --> pdb=" O ILE H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 551 Processing helix chain 'H' and resid 580 through 583 No H-bonds generated for 'chain 'H' and resid 580 through 583' Processing helix chain 'H' and resid 586 through 597 removed outlier: 4.329A pdb=" N ARG H 592 " --> pdb=" O CYS H 588 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL H 593 " --> pdb=" O LEU H 589 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE H 594 " --> pdb=" O ALA H 590 " (cutoff:3.500A) Processing helix chain 'H' and resid 607 through 615 removed outlier: 4.365A pdb=" N THR H 611 " --> pdb=" O GLU H 607 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE H 612 " --> pdb=" O LYS H 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 13 removed outlier: 3.642A pdb=" N ASN H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 22 removed outlier: 3.557A pdb=" N LYS H 21 " --> pdb=" O ARG H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.637A pdb=" N ILE H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 35' Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 54 through 63 Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 96 through 104 Processing helix chain 'H' and resid 119 through 126 removed outlier: 4.147A pdb=" N ASP H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 137 Processing helix chain 'H' and resid 152 through 158 Processing helix chain 'H' and resid 162 through 170 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.608A pdb=" N TYR H 204 " --> pdb=" O MET H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 224 Processing helix chain 'H' and resid 227 through 235 removed outlier: 4.350A pdb=" N HIS H 235 " --> pdb=" O ASP H 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'R' and resid 54 through 57 No H-bonds generated for 'chain 'R' and resid 54 through 57' Processing helix chain 'R' and resid 81 through 90 removed outlier: 4.127A pdb=" N THR R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 Processing helix chain 'U' and resid 38 through 40 No H-bonds generated for 'chain 'U' and resid 38 through 40' Processing helix chain 'U' and resid 56 through 59 No H-bonds generated for 'chain 'U' and resid 56 through 59' Processing sheet with id=9, first strand: chain 'C' and resid 40 through 46 No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'C' and resid 57 through 64 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'C' and resid 74 through 78 No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'U' and resid 2 through 6 No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'U' and resid 12 through 16 No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'U' and resid 42 through 44 No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'U' and resid 66 through 70 No H-bonds generated for sheet with id=15 Processing sheet with id=20, first strand: chain 'A' and resid 507 through 512 No H-bonds generated for sheet with id=20 Processing sheet with id=22, first strand: chain 'A' and resid 552 through 556 No H-bonds generated for sheet with id=22 Processing sheet with id=A, first strand: chain 'A' and resid 561 through 566 Processing sheet with id=B, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=23, first strand: chain 'R' and resid 70 through 72 No H-bonds generated for sheet with id=23 Processing sheet with id=24, first strand: chain 'R' and resid 78 through 80 No H-bonds generated for sheet with id=24 Processing sheet with id=8, first strand: chain 'C' and resid 28 through 32 No H-bonds generated for sheet with id=8 Processing sheet with id=1, first strand: chain 'G' and resid 42 through 45 No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'G' and resid 73 through 79 No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'G' and resid 2 through 8 No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'G' and resid 12 through 19 No H-bonds generated for sheet with id=4 Processing sheet with id=6, first strand: chain 'D' and resid 18 through 23 No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'D' and resid 59 through 62 No H-bonds generated for sheet with id=7 518 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4102 1.34 - 1.47: 2968 1.47 - 1.59: 5584 1.59 - 1.71: 0 1.71 - 1.84: 124 Bond restraints: 12778 Sorted by residual: bond pdb=" N ARG A 249 " pdb=" CA ARG A 249 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.32e-02 5.74e+03 1.48e+01 bond pdb=" N ILE C 94 " pdb=" CA ILE C 94 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.19e-02 7.06e+03 1.30e+01 bond pdb=" C PRO H 377 " pdb=" N MET H 378 " ideal model delta sigma weight residual 1.334 1.281 0.053 1.61e-02 3.86e+03 1.07e+01 bond pdb=" N VAL R 39 " pdb=" CA VAL R 39 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.47e+00 bond pdb=" N VAL R 38 " pdb=" CA VAL R 38 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.56e+00 ... (remaining 12773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 17181 2.57 - 5.15: 207 5.15 - 7.72: 30 7.72 - 10.29: 11 10.29 - 12.87: 2 Bond angle restraints: 17431 Sorted by residual: angle pdb=" CA ASN A 169 " pdb=" C ASN A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 118.44 108.40 10.04 1.41e+00 5.03e-01 5.07e+01 angle pdb=" CA PRO H 531 " pdb=" N PRO H 531 " pdb=" CD PRO H 531 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N LEU U 73 " pdb=" CA LEU U 73 " pdb=" CB LEU U 73 " ideal model delta sigma weight residual 111.56 104.05 7.51 1.52e+00 4.33e-01 2.44e+01 angle pdb=" C ARG A 249 " pdb=" CA ARG A 249 " pdb=" CB ARG A 249 " ideal model delta sigma weight residual 110.11 101.91 8.20 1.90e+00 2.77e-01 1.86e+01 angle pdb=" O ASN A 169 " pdb=" C ASN A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 122.39 128.45 -6.06 1.48e+00 4.57e-01 1.67e+01 ... (remaining 17426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 6607 16.85 - 33.71: 717 33.71 - 50.56: 231 50.56 - 67.42: 44 67.42 - 84.27: 9 Dihedral angle restraints: 7608 sinusoidal: 2540 harmonic: 5068 Sorted by residual: dihedral pdb=" CA TYR H 500 " pdb=" C TYR H 500 " pdb=" N PRO H 501 " pdb=" CA PRO H 501 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA VAL H 502 " pdb=" C VAL H 502 " pdb=" N CYS H 503 " pdb=" CA CYS H 503 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" N ASP C 91 " pdb=" CA ASP C 91 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1826 0.060 - 0.119: 237 0.119 - 0.179: 22 0.179 - 0.238: 5 0.238 - 0.298: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA GLU A 208 " pdb=" N GLU A 208 " pdb=" C GLU A 208 " pdb=" CB GLU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA TRP R 35 " pdb=" N TRP R 35 " pdb=" C TRP R 35 " pdb=" CB TRP R 35 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2089 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 530 " 0.077 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO H 531 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO H 531 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 531 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 93 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C CYS C 93 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS C 93 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE C 94 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 434 " -0.055 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO H 435 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO H 435 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 435 " -0.045 5.00e-02 4.00e+02 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 69 2.57 - 3.15: 10220 3.15 - 3.73: 18924 3.73 - 4.32: 23627 4.32 - 4.90: 39335 Nonbonded interactions: 92175 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.987 2.230 nonbonded pdb=" N GLN H 437 " pdb=" OE1 GLN H 437 " model vdw 2.260 3.120 nonbonded pdb=" OG SER A 591 " pdb=" O THR A 593 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN C 115 " pdb=" O PRO R 95 " model vdw 2.296 3.120 nonbonded pdb=" NH2 ARG R 91 " pdb=" OD1 ASN R 98 " model vdw 2.304 3.120 ... (remaining 92170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 3.460 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 0.266 12792 Z= 0.239 Angle : 0.748 12.867 17439 Z= 0.396 Chirality : 0.043 0.298 2092 Planarity : 0.006 0.123 2224 Dihedral : 16.340 84.272 4297 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.26 % Allowed : 24.94 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -1.10 (0.20), residues: 1678 helix: 0.44 (0.18), residues: 871 sheet: -1.05 (0.66), residues: 72 loop : -2.18 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 35 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.002 PHE A 202 TYR 0.023 0.002 TYR A 558 ARG 0.013 0.001 ARG A 249 Details of bonding type rmsd link_TRANS : bond 0.01202 ( 1) link_TRANS : angle 3.57952 ( 2) hydrogen bonds : bond 0.11034 ( 511) hydrogen bonds : angle 4.68541 ( 1548) metal coordination : bond 0.08311 ( 11) metal coordination : angle 4.46020 ( 6) covalent geometry : bond 0.00432 (12778) covalent geometry : angle 0.74261 (17431) Misc. bond : bond 0.06650 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6301 (mt-10) REVERT: A 470 THR cc_start: 0.5829 (t) cc_final: 0.4718 (m) REVERT: H 412 MET cc_start: 0.7356 (mmm) cc_final: 0.7122 (mmm) REVERT: D 108 ASN cc_start: 0.7969 (t0) cc_final: 0.7737 (t0) outliers start: 15 outliers final: 7 residues processed: 266 average time/residue: 0.2271 time to fit residues: 87.4756 Evaluate side-chains 249 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.6980 chunk 128 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 132 optimal weight: 0.0070 chunk 51 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 320 HIS H 100 GLN H 368 GLN H 467 GLN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.168477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137496 restraints weight = 32628.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136458 restraints weight = 17687.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138112 restraints weight = 14266.187| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12792 Z= 0.116 Angle : 0.569 13.601 17439 Z= 0.286 Chirality : 0.038 0.185 2092 Planarity : 0.005 0.065 2224 Dihedral : 5.251 55.035 1823 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.54 % Allowed : 24.85 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1678 helix: 0.77 (0.18), residues: 889 sheet: -0.88 (0.62), residues: 81 loop : -2.15 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 33 HIS 0.007 0.001 HIS A 320 PHE 0.019 0.001 PHE H 408 TYR 0.017 0.001 TYR H 601 ARG 0.004 0.000 ARG D 63 Details of bonding type rmsd link_TRANS : bond 0.00036 ( 1) link_TRANS : angle 0.06158 ( 2) hydrogen bonds : bond 0.04392 ( 511) hydrogen bonds : angle 3.92858 ( 1548) metal coordination : bond 0.00892 ( 11) metal coordination : angle 3.58548 ( 6) covalent geometry : bond 0.00250 (12778) covalent geometry : angle 0.56492 (17431) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8189 (mmp) cc_final: 0.7934 (mmp) REVERT: A 582 MET cc_start: 0.6437 (mmm) cc_final: 0.6233 (mmm) REVERT: A 599 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7128 (mt) REVERT: H 515 ILE cc_start: 0.8078 (mp) cc_final: 0.7868 (mp) REVERT: H 545 ASN cc_start: 0.8221 (m-40) cc_final: 0.7998 (m-40) REVERT: C 83 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7629 (p-80) REVERT: D 33 ARG cc_start: 0.7565 (ttm170) cc_final: 0.7361 (mmm160) outliers start: 42 outliers final: 20 residues processed: 260 average time/residue: 0.2265 time to fit residues: 86.8255 Evaluate side-chains 254 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 165 optimal weight: 0.0470 chunk 24 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 320 HIS H 368 GLN H 467 GLN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.165865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135466 restraints weight = 44819.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134474 restraints weight = 26181.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136007 restraints weight = 19279.799| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12792 Z= 0.135 Angle : 0.561 13.584 17439 Z= 0.285 Chirality : 0.039 0.182 2092 Planarity : 0.005 0.059 2224 Dihedral : 4.386 38.059 1810 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.13 % Allowed : 24.43 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1678 helix: 0.86 (0.18), residues: 893 sheet: -0.81 (0.63), residues: 81 loop : -2.11 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.022 0.001 PHE A 202 TYR 0.015 0.001 TYR H 343 ARG 0.004 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00056 ( 1) link_TRANS : angle 0.00633 ( 2) hydrogen bonds : bond 0.04874 ( 511) hydrogen bonds : angle 3.90301 ( 1548) metal coordination : bond 0.00764 ( 11) metal coordination : angle 2.72210 ( 6) covalent geometry : bond 0.00296 (12778) covalent geometry : angle 0.55865 (17431) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8184 (mmp) cc_final: 0.7952 (mmp) REVERT: A 582 MET cc_start: 0.6496 (mmm) cc_final: 0.6283 (mmm) REVERT: A 599 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7118 (mp) REVERT: H 378 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5895 (ptm) REVERT: H 434 ASP cc_start: 0.7383 (t0) cc_final: 0.7099 (t70) REVERT: H 515 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.8020 (mp) REVERT: C 83 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7632 (p-80) REVERT: D 33 ARG cc_start: 0.7627 (ttm170) cc_final: 0.7392 (mmm160) REVERT: R 84 ILE cc_start: 0.4217 (OUTLIER) cc_final: 0.3993 (mt) outliers start: 49 outliers final: 29 residues processed: 267 average time/residue: 0.2205 time to fit residues: 86.6188 Evaluate side-chains 267 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 378 MET Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 508 LEU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 94 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 152 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 274 HIS A 320 HIS H 368 GLN H 467 GLN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133613 restraints weight = 31568.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132878 restraints weight = 19051.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134613 restraints weight = 13343.263| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12792 Z= 0.146 Angle : 0.568 13.556 17439 Z= 0.288 Chirality : 0.039 0.184 2092 Planarity : 0.005 0.057 2224 Dihedral : 4.417 26.518 1810 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.55 % Allowed : 24.85 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1678 helix: 0.86 (0.18), residues: 896 sheet: -1.16 (0.62), residues: 84 loop : -2.02 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.022 0.001 PHE A 202 TYR 0.016 0.001 TYR H 343 ARG 0.005 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00042 ( 1) link_TRANS : angle 0.05886 ( 2) hydrogen bonds : bond 0.05108 ( 511) hydrogen bonds : angle 3.92360 ( 1548) metal coordination : bond 0.00810 ( 11) metal coordination : angle 2.35727 ( 6) covalent geometry : bond 0.00317 (12778) covalent geometry : angle 0.56649 (17431) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8140 (mmp) cc_final: 0.7889 (mmp) REVERT: A 599 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7056 (mt) REVERT: A 622 MET cc_start: 0.4978 (ptp) cc_final: 0.4556 (ptp) REVERT: H 437 GLN cc_start: 0.7623 (mp10) cc_final: 0.7293 (mp10) REVERT: H 515 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (mp) REVERT: C 83 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7662 (p-80) outliers start: 54 outliers final: 31 residues processed: 270 average time/residue: 0.2154 time to fit residues: 85.1343 Evaluate side-chains 269 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 157 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 310 HIS A 320 HIS H 467 GLN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.162843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132599 restraints weight = 39032.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132200 restraints weight = 22152.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.133270 restraints weight = 16923.565| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12792 Z= 0.169 Angle : 0.602 13.247 17439 Z= 0.303 Chirality : 0.040 0.184 2092 Planarity : 0.005 0.057 2224 Dihedral : 4.504 26.700 1809 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 5.39 % Allowed : 24.26 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1678 helix: 0.84 (0.18), residues: 892 sheet: -0.84 (0.65), residues: 75 loop : -2.02 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.002 PHE A 202 TYR 0.020 0.002 TYR H 158 ARG 0.007 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00050 ( 1) link_TRANS : angle 0.05983 ( 2) hydrogen bonds : bond 0.05597 ( 511) hydrogen bonds : angle 4.04015 ( 1548) metal coordination : bond 0.00938 ( 11) metal coordination : angle 2.18145 ( 6) covalent geometry : bond 0.00376 (12778) covalent geometry : angle 0.60040 (17431) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8130 (mmp) cc_final: 0.7815 (mmp) REVERT: A 398 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 566 MET cc_start: 0.2248 (mmm) cc_final: 0.1712 (mmp) REVERT: A 599 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 622 MET cc_start: 0.5597 (ptp) cc_final: 0.5304 (ptp) REVERT: H 515 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (mp) REVERT: H 526 SER cc_start: 0.7680 (p) cc_final: 0.7414 (t) REVERT: C 83 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7697 (p-80) outliers start: 64 outliers final: 42 residues processed: 291 average time/residue: 0.2211 time to fit residues: 94.4936 Evaluate side-chains 294 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 614 SER Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain R residue 79 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 161 HIS ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132514 restraints weight = 35522.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131126 restraints weight = 21670.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133416 restraints weight = 15362.320| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12792 Z= 0.153 Angle : 0.588 13.187 17439 Z= 0.299 Chirality : 0.039 0.215 2092 Planarity : 0.005 0.057 2224 Dihedral : 4.492 28.095 1809 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.66 % Rotamer: Outliers : 5.14 % Allowed : 24.68 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1678 helix: 0.85 (0.18), residues: 892 sheet: -0.77 (0.66), residues: 75 loop : -1.97 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 87 HIS 0.007 0.001 HIS A 347 PHE 0.021 0.001 PHE A 10 TYR 0.016 0.001 TYR H 158 ARG 0.008 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 1) link_TRANS : angle 0.04264 ( 2) hydrogen bonds : bond 0.05361 ( 511) hydrogen bonds : angle 4.00557 ( 1548) metal coordination : bond 0.00772 ( 11) metal coordination : angle 1.68344 ( 6) covalent geometry : bond 0.00339 (12778) covalent geometry : angle 0.58699 (17431) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8175 (mmp) cc_final: 0.7811 (mmp) REVERT: A 398 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 599 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7095 (mt) REVERT: A 622 MET cc_start: 0.5457 (ptp) cc_final: 0.5175 (ptp) REVERT: H 515 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7984 (mp) REVERT: H 526 SER cc_start: 0.7677 (p) cc_final: 0.7409 (t) REVERT: C 83 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7664 (p-80) outliers start: 61 outliers final: 41 residues processed: 278 average time/residue: 0.2262 time to fit residues: 91.8797 Evaluate side-chains 285 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 320 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.0670 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 164 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 151 optimal weight: 0.0370 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 150 HIS H 161 HIS H 226 HIS ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134319 restraints weight = 42786.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133672 restraints weight = 25490.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.134653 restraints weight = 20213.862| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12792 Z= 0.116 Angle : 0.567 13.476 17439 Z= 0.284 Chirality : 0.038 0.188 2092 Planarity : 0.005 0.055 2224 Dihedral : 4.321 28.573 1809 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 4.13 % Allowed : 25.95 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1678 helix: 1.06 (0.18), residues: 881 sheet: -0.75 (0.66), residues: 75 loop : -1.94 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 14 HIS 0.006 0.001 HIS C 61 PHE 0.020 0.001 PHE A 10 TYR 0.014 0.001 TYR D 79 ARG 0.007 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.01079 ( 2) hydrogen bonds : bond 0.04613 ( 511) hydrogen bonds : angle 3.87628 ( 1548) metal coordination : bond 0.00493 ( 11) metal coordination : angle 1.25680 ( 6) covalent geometry : bond 0.00257 (12778) covalent geometry : angle 0.56629 (17431) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8107 (mmp) cc_final: 0.7725 (mmp) REVERT: A 599 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7105 (mp) REVERT: A 622 MET cc_start: 0.5689 (ptp) cc_final: 0.5472 (ptp) REVERT: H 515 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (mp) REVERT: H 526 SER cc_start: 0.7688 (p) cc_final: 0.7415 (t) REVERT: C 83 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7689 (p-80) outliers start: 49 outliers final: 36 residues processed: 272 average time/residue: 0.2315 time to fit residues: 92.4490 Evaluate side-chains 277 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 320 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 91 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 24 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 141 optimal weight: 0.0370 chunk 100 optimal weight: 0.0670 chunk 7 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 320 HIS H 161 HIS H 226 HIS ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.163985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133718 restraints weight = 38786.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132577 restraints weight = 25538.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133949 restraints weight = 20560.834| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12792 Z= 0.124 Angle : 0.576 13.921 17439 Z= 0.287 Chirality : 0.038 0.184 2092 Planarity : 0.005 0.060 2224 Dihedral : 4.242 28.329 1809 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 4.04 % Allowed : 26.12 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1678 helix: 1.06 (0.18), residues: 889 sheet: -0.68 (0.66), residues: 75 loop : -1.94 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 14 HIS 0.009 0.001 HIS A 320 PHE 0.016 0.001 PHE A 202 TYR 0.013 0.001 TYR D 79 ARG 0.008 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00025 ( 1) link_TRANS : angle 0.01634 ( 2) hydrogen bonds : bond 0.04692 ( 511) hydrogen bonds : angle 3.85004 ( 1548) metal coordination : bond 0.00607 ( 11) metal coordination : angle 1.25026 ( 6) covalent geometry : bond 0.00276 (12778) covalent geometry : angle 0.57596 (17431) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8119 (mmp) cc_final: 0.7773 (mmp) REVERT: A 599 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7082 (mp) REVERT: A 622 MET cc_start: 0.5730 (ptp) cc_final: 0.5527 (ptp) REVERT: H 515 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7998 (mp) REVERT: H 526 SER cc_start: 0.7702 (p) cc_final: 0.7439 (t) REVERT: C 83 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7750 (p-80) outliers start: 48 outliers final: 37 residues processed: 262 average time/residue: 0.2180 time to fit residues: 84.4791 Evaluate side-chains 275 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 320 MET Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 614 SER Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 25 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.0050 chunk 77 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS H 303 ASN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133304 restraints weight = 32040.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132836 restraints weight = 20140.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134689 restraints weight = 14686.861| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12792 Z= 0.128 Angle : 0.592 13.877 17439 Z= 0.294 Chirality : 0.039 0.186 2092 Planarity : 0.005 0.063 2224 Dihedral : 4.249 27.965 1809 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 4.04 % Allowed : 25.86 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1678 helix: 1.04 (0.18), residues: 891 sheet: -0.70 (0.66), residues: 75 loop : -1.89 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 14 HIS 0.009 0.001 HIS R 82 PHE 0.028 0.001 PHE A 112 TYR 0.014 0.001 TYR D 79 ARG 0.009 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.02135 ( 2) hydrogen bonds : bond 0.04650 ( 511) hydrogen bonds : angle 3.85567 ( 1548) metal coordination : bond 0.01513 ( 11) metal coordination : angle 5.74510 ( 6) covalent geometry : bond 0.00286 (12778) covalent geometry : angle 0.58261 (17431) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8051 (mmp) cc_final: 0.7703 (mmp) REVERT: A 599 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7017 (mp) REVERT: A 622 MET cc_start: 0.5218 (ptp) cc_final: 0.4984 (ptp) REVERT: H 56 MET cc_start: 0.5396 (tpp) cc_final: 0.4673 (tmm) REVERT: H 515 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7993 (mp) REVERT: H 526 SER cc_start: 0.7683 (p) cc_final: 0.7409 (t) REVERT: C 83 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7685 (p-80) outliers start: 48 outliers final: 43 residues processed: 262 average time/residue: 0.2195 time to fit residues: 84.8975 Evaluate side-chains 281 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 235 HIS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 320 MET Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 91 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 126 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 168 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.160038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126019 restraints weight = 24481.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128777 restraints weight = 13256.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130757 restraints weight = 8469.239| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12792 Z= 0.204 Angle : 0.666 13.508 17439 Z= 0.337 Chirality : 0.042 0.186 2092 Planarity : 0.005 0.080 2224 Dihedral : 4.715 27.765 1809 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 3.71 % Allowed : 26.37 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1678 helix: 0.70 (0.18), residues: 888 sheet: -0.53 (0.67), residues: 69 loop : -1.97 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 14 HIS 0.009 0.001 HIS A 347 PHE 0.025 0.002 PHE A 112 TYR 0.020 0.002 TYR H 158 ARG 0.008 0.001 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00072 ( 1) link_TRANS : angle 0.08812 ( 2) hydrogen bonds : bond 0.06428 ( 511) hydrogen bonds : angle 4.25474 ( 1548) metal coordination : bond 0.01317 ( 11) metal coordination : angle 4.65794 ( 6) covalent geometry : bond 0.00454 (12778) covalent geometry : angle 0.66089 (17431) Misc. bond : bond 0.00068 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8122 (mmp) cc_final: 0.7771 (mmp) REVERT: A 268 GLN cc_start: 0.7456 (tp40) cc_final: 0.6951 (tp40) REVERT: A 517 TRP cc_start: 0.7755 (m100) cc_final: 0.7411 (m100) REVERT: A 599 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7188 (mp) REVERT: H 56 MET cc_start: 0.5437 (tpp) cc_final: 0.4814 (tmm) REVERT: H 412 MET cc_start: 0.7294 (mmm) cc_final: 0.7014 (mmm) REVERT: H 434 ASP cc_start: 0.7311 (t0) cc_final: 0.7067 (t70) REVERT: H 515 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8014 (mp) REVERT: H 526 SER cc_start: 0.7698 (p) cc_final: 0.7459 (t) REVERT: C 83 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7645 (p-80) outliers start: 44 outliers final: 37 residues processed: 271 average time/residue: 0.2315 time to fit residues: 91.7582 Evaluate side-chains 283 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain H residue 320 MET Chi-restraints excluded: chain H residue 336 ASP Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 515 ILE Chi-restraints excluded: chain H residue 544 MET Chi-restraints excluded: chain H residue 588 CYS Chi-restraints excluded: chain H residue 614 SER Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain G residue 91 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 94 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.0570 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 0.0010 chunk 163 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130076 restraints weight = 39785.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128120 restraints weight = 26346.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130520 restraints weight = 18773.829| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 12792 Z= 0.201 Angle : 0.899 59.199 17439 Z= 0.511 Chirality : 0.045 0.933 2092 Planarity : 0.006 0.077 2224 Dihedral : 4.831 46.832 1809 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.88 % Favored : 92.00 % Rotamer: Outliers : 3.71 % Allowed : 26.96 % Favored : 69.33 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1678 helix: 0.69 (0.18), residues: 890 sheet: -0.53 (0.67), residues: 69 loop : -1.99 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 14 HIS 0.009 0.001 HIS A 347 PHE 0.021 0.002 PHE A 202 TYR 0.020 0.002 TYR A 203 ARG 0.004 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00029 ( 1) link_TRANS : angle 0.12210 ( 2) hydrogen bonds : bond 0.06288 ( 511) hydrogen bonds : angle 4.25211 ( 1548) metal coordination : bond 0.01279 ( 11) metal coordination : angle 4.59694 ( 6) covalent geometry : bond 0.00437 (12778) covalent geometry : angle 0.89539 (17431) Misc. bond : bond 0.00033 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.96 seconds wall clock time: 85 minutes 59.98 seconds (5159.98 seconds total)