Starting phenix.real_space_refine on Wed Jul 30 13:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7r_18230/07_2025/8q7r_18230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7r_18230/07_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_18230/07_2025/8q7r_18230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7r_18230/07_2025/8q7r_18230.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7r_18230/07_2025/8q7r_18230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7r_18230/07_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-5711/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: 8.69, per 1000 atoms: 0.69 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: 3.33 Conformation dependent library (CDL) restraints added in 1.9 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: 1.29 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: 2.99 Time building geometry restraints manager: 4.07 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: 4.020 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: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.560 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- 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 : 1.446 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: 0.2441 time to fit residues: 94.1451 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 : 1.373 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138517 restraints weight = 32628.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135756 restraints weight = 20741.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138197 restraints weight = 15837.072| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 55.032 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 0.06076 ( 2) hydrogen bonds : bond 0.04392 ( 511) hydrogen bonds : angle 3.92854 ( 1548) metal coordination : bond 0.00892 ( 11) metal coordination : angle 3.58522 ( 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 : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8181 (mmp) cc_final: 0.7926 (mmp) REVERT: A 582 MET cc_start: 0.6573 (mmm) cc_final: 0.6337 (mmm) REVERT: A 599 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7205 (mt) REVERT: H 515 ILE cc_start: 0.8078 (mp) cc_final: 0.7865 (mp) REVERT: H 545 ASN cc_start: 0.8249 (m-40) cc_final: 0.8018 (m-40) REVERT: C 83 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7633 (p-80) REVERT: D 33 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7362 (mmm160) outliers start: 42 outliers final: 20 residues processed: 260 average time/residue: 0.2535 time to fit residues: 98.5958 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 : 1.276 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 0.0060 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 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 = 0.4174 r_free = 0.4174 target = 0.165172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134803 restraints weight = 44736.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134120 restraints weight = 25227.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135434 restraints weight = 18505.167| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 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 = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1292 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= 0.143 Angle : 0.570 13.578 17439 Z= 0.290 Chirality : 0.039 0.182 2092 Planarity : 0.005 0.060 2224 Dihedral : 4.416 38.166 1810 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.13 % Allowed : 24.60 % Favored : 71.27 % 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: -0.65 (0.21), residues: 1678 helix: 0.83 (0.18), residues: 893 sheet: -1.05 (0.62), residues: 84 loop : -2.09 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 27 HIS 0.008 0.001 HIS A 320 PHE 0.024 0.001 PHE A 202 TYR 0.017 0.001 TYR H 343 ARG 0.004 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00010 ( 1) link_TRANS : angle 0.01551 ( 2) hydrogen bonds : bond 0.05058 ( 511) hydrogen bonds : angle 3.93784 ( 1548) metal coordination : bond 0.00798 ( 11) metal coordination : angle 2.66967 ( 6) covalent geometry : bond 0.00315 (12778) covalent geometry : angle 0.56805 (17431) Misc. bond : bond 0.00047 ( 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 292 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8187 (mmp) cc_final: 0.7943 (mmp) REVERT: A 364 PHE cc_start: 0.7047 (m-80) cc_final: 0.6825 (m-80) REVERT: A 582 MET cc_start: 0.6606 (mmm) cc_final: 0.6365 (mmm) REVERT: A 599 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7070 (mp) REVERT: A 622 MET cc_start: 0.5295 (ptp) cc_final: 0.4815 (ptp) REVERT: H 434 ASP cc_start: 0.7401 (t0) cc_final: 0.7105 (t70) REVERT: H 515 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8017 (mp) REVERT: C 83 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7657 (p-80) REVERT: D 33 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7397 (mmm160) REVERT: R 84 ILE cc_start: 0.4239 (OUTLIER) cc_final: 0.4008 (mt) outliers start: 49 outliers final: 27 residues processed: 268 average time/residue: 0.2182 time to fit residues: 86.3705 Evaluate side-chains 267 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 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 576 MET 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 422 ILE Chi-restraints excluded: chain H residue 502 VAL 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 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: 0.9990 chunk 145 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 152 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 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 = 0.4160 r_free = 0.4160 target = 0.164054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133334 restraints weight = 31580.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132645 restraints weight = 20270.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134396 restraints weight = 15435.134| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12792 Z= 0.143 Angle : 0.567 13.484 17439 Z= 0.286 Chirality : 0.039 0.186 2092 Planarity : 0.005 0.058 2224 Dihedral : 4.406 26.725 1810 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.13 % Allowed : 25.11 % Favored : 70.77 % 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: -0.62 (0.20), residues: 1678 helix: 0.82 (0.18), residues: 901 sheet: -0.93 (0.63), residues: 81 loop : -2.05 (0.22), residues: 696 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 0.021 0.001 PHE A 202 TYR 0.016 0.001 TYR H 343 ARG 0.007 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 0.06595 ( 2) hydrogen bonds : bond 0.05090 ( 511) hydrogen bonds : angle 3.92396 ( 1548) metal coordination : bond 0.00819 ( 11) metal coordination : angle 2.35309 ( 6) covalent geometry : bond 0.00316 (12778) covalent geometry : angle 0.56554 (17431) Misc. bond : bond 0.00044 ( 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 289 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8142 (mmp) cc_final: 0.7884 (mmp) REVERT: A 364 PHE cc_start: 0.6978 (m-80) cc_final: 0.6703 (m-80) REVERT: A 599 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7011 (mt) REVERT: A 622 MET cc_start: 0.5009 (ptp) cc_final: 0.4574 (ptp) REVERT: H 434 ASP cc_start: 0.7341 (t0) cc_final: 0.7075 (t70) REVERT: H 515 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7989 (mp) REVERT: C 83 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7691 (p-80) REVERT: D 105 MET cc_start: 0.6879 (mtt) cc_final: 0.6599 (mtp) outliers start: 49 outliers final: 29 residues processed: 267 average time/residue: 0.2333 time to fit residues: 91.6704 Evaluate side-chains 268 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 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 190 HIS 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 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: 0.0980 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 0.0000 chunk 83 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 467 GLN ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.165651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135265 restraints weight = 39246.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134316 restraints weight = 22767.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136099 restraints weight = 16319.125| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1807 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 : 0.554 13.680 17439 Z= 0.275 Chirality : 0.038 0.186 2092 Planarity : 0.004 0.054 2224 Dihedral : 4.211 27.024 1809 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 4.63 % Allowed : 24.68 % Favored : 70.68 % 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: -0.44 (0.21), residues: 1678 helix: 1.00 (0.18), residues: 894 sheet: -0.69 (0.65), residues: 75 loop : -2.00 (0.22), residues: 709 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 0.015 0.001 PHE A 202 TYR 0.013 0.001 TYR H 601 ARG 0.007 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.01817 ( 2) hydrogen bonds : bond 0.04513 ( 511) hydrogen bonds : angle 3.80072 ( 1548) metal coordination : bond 0.00729 ( 11) metal coordination : angle 1.92827 ( 6) covalent geometry : bond 0.00254 (12778) covalent geometry : angle 0.55291 (17431) Misc. bond : bond 0.00025 ( 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 298 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8117 (mmp) cc_final: 0.7822 (mmp) REVERT: A 364 PHE cc_start: 0.6990 (m-80) cc_final: 0.6736 (m-80) REVERT: A 566 MET cc_start: 0.1799 (mmm) cc_final: 0.1186 (mmp) REVERT: A 599 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6985 (mp) REVERT: A 622 MET cc_start: 0.5401 (ptp) cc_final: 0.5054 (ptp) REVERT: H 434 ASP cc_start: 0.7359 (t0) cc_final: 0.7086 (t70) REVERT: H 515 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7990 (mp) REVERT: H 526 SER cc_start: 0.7670 (p) cc_final: 0.7391 (t) REVERT: H 600 TYR cc_start: 0.6998 (t80) cc_final: 0.6740 (t80) REVERT: U 1 MET cc_start: 0.3523 (tpt) cc_final: 0.3268 (tpt) REVERT: C 83 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7673 (p-80) outliers start: 55 outliers final: 36 residues processed: 277 average time/residue: 0.2235 time to fit residues: 91.3232 Evaluate side-chains 276 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LYS 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 270 MET 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 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 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 459 LEU Chi-restraints excluded: chain H residue 502 VAL 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 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 G residue 41 GLU 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: 0.6980 chunk 27 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 111 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 320 HIS ** H 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.164268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133490 restraints weight = 35656.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132999 restraints weight = 19367.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.134214 restraints weight = 16206.985| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12792 Z= 0.136 Angle : 0.561 13.842 17439 Z= 0.283 Chirality : 0.038 0.184 2092 Planarity : 0.005 0.053 2224 Dihedral : 4.280 27.183 1809 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 4.89 % Allowed : 24.18 % Favored : 70.94 % 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: -0.45 (0.21), residues: 1678 helix: 0.94 (0.18), residues: 898 sheet: -0.60 (0.67), residues: 75 loop : -1.96 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 87 HIS 0.008 0.001 HIS A 320 PHE 0.021 0.001 PHE A 10 TYR 0.014 0.001 TYR H 343 ARG 0.007 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00049 ( 1) link_TRANS : angle 0.02442 ( 2) hydrogen bonds : bond 0.04904 ( 511) hydrogen bonds : angle 3.83383 ( 1548) metal coordination : bond 0.00689 ( 11) metal coordination : angle 1.97536 ( 6) covalent geometry : bond 0.00303 (12778) covalent geometry : angle 0.56035 (17431) Misc. bond : bond 0.00035 ( 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 298 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8145 (mmp) cc_final: 0.7840 (mmp) REVERT: A 364 PHE cc_start: 0.7037 (m-80) cc_final: 0.6747 (m-80) REVERT: A 566 MET cc_start: 0.2118 (mmm) cc_final: 0.1750 (mmp) REVERT: A 599 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7126 (mp) REVERT: A 622 MET cc_start: 0.5386 (ptp) cc_final: 0.5072 (ptp) REVERT: H 434 ASP cc_start: 0.7311 (t0) cc_final: 0.7061 (t70) REVERT: H 515 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8002 (mp) REVERT: H 526 SER cc_start: 0.7661 (p) cc_final: 0.7381 (t) REVERT: H 600 TYR cc_start: 0.7069 (t80) cc_final: 0.6836 (t80) REVERT: U 1 MET cc_start: 0.3550 (tpt) cc_final: 0.3225 (tpt) REVERT: C 83 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7700 (p-80) outliers start: 58 outliers final: 40 residues processed: 271 average time/residue: 0.2328 time to fit residues: 92.6613 Evaluate side-chains 282 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP 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 164 LEU Chi-restraints excluded: chain A residue 190 HIS 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 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 579 THR 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 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 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 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 81 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 75 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 85 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS A 320 HIS H 150 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 = 0.4173 r_free = 0.4173 target = 0.165149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135240 restraints weight = 42943.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134050 restraints weight = 27632.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135542 restraints weight = 20067.587| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 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 = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12792 Z= 0.115 Angle : 0.551 13.868 17439 Z= 0.276 Chirality : 0.038 0.249 2092 Planarity : 0.004 0.050 2224 Dihedral : 4.186 27.344 1809 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 3.88 % Allowed : 25.36 % Favored : 70.77 % 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: -0.32 (0.21), residues: 1678 helix: 1.10 (0.18), residues: 890 sheet: -0.47 (0.68), residues: 75 loop : -1.96 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 14 HIS 0.007 0.001 HIS A 320 PHE 0.015 0.001 PHE A 202 TYR 0.012 0.001 TYR D 79 ARG 0.006 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.02273 ( 2) hydrogen bonds : bond 0.04437 ( 511) hydrogen bonds : angle 3.76808 ( 1548) metal coordination : bond 0.00501 ( 11) metal coordination : angle 1.23867 ( 6) covalent geometry : bond 0.00254 (12778) covalent geometry : angle 0.55075 (17431) Misc. bond : bond 0.00027 ( 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 291 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8084 (mmp) cc_final: 0.7769 (mmp) REVERT: A 364 PHE cc_start: 0.7070 (m-80) cc_final: 0.6791 (m-80) REVERT: A 599 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7143 (mp) REVERT: A 622 MET cc_start: 0.5415 (ptp) cc_final: 0.5144 (ptp) REVERT: H 348 TYR cc_start: 0.7334 (m-10) cc_final: 0.6974 (m-80) REVERT: H 434 ASP cc_start: 0.7357 (t0) cc_final: 0.7111 (t70) REVERT: H 488 LEU cc_start: 0.8187 (mt) cc_final: 0.7974 (mt) REVERT: H 515 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8011 (mp) REVERT: H 526 SER cc_start: 0.7693 (p) cc_final: 0.7406 (t) REVERT: H 600 TYR cc_start: 0.6991 (t80) cc_final: 0.6738 (t80) REVERT: U 1 MET cc_start: 0.3535 (tpt) cc_final: 0.3213 (tpt) REVERT: C 83 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7689 (p-80) REVERT: D 105 MET cc_start: 0.6968 (mtt) cc_final: 0.6733 (mtp) outliers start: 46 outliers final: 33 residues processed: 270 average time/residue: 0.2253 time to fit residues: 90.0775 Evaluate side-chains 278 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 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 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 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 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 95 SER 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: 0.0870 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 166 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 0.0060 overall best weight: 0.4432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 320 HIS ** 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 = 0.4171 r_free = 0.4171 target = 0.164926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134927 restraints weight = 38856.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133633 restraints weight = 24151.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135820 restraints weight = 16722.272| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12792 Z= 0.120 Angle : 0.566 14.066 17439 Z= 0.282 Chirality : 0.038 0.183 2092 Planarity : 0.005 0.050 2224 Dihedral : 4.159 27.446 1809 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 4.04 % Allowed : 25.36 % 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: -0.28 (0.21), residues: 1678 helix: 1.14 (0.18), residues: 891 sheet: -0.65 (0.67), residues: 75 loop : -1.92 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 87 HIS 0.006 0.001 HIS C 61 PHE 0.025 0.001 PHE A 112 TYR 0.012 0.001 TYR D 79 ARG 0.008 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.00753 ( 2) hydrogen bonds : bond 0.04492 ( 511) hydrogen bonds : angle 3.76623 ( 1548) metal coordination : bond 0.00512 ( 11) metal coordination : angle 1.18057 ( 6) covalent geometry : bond 0.00270 (12778) covalent geometry : angle 0.56548 (17431) Misc. bond : bond 0.00022 ( 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 294 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8084 (mmp) cc_final: 0.7760 (mmp) REVERT: A 364 PHE cc_start: 0.7086 (m-80) cc_final: 0.6780 (m-80) REVERT: A 370 LYS cc_start: 0.8168 (mttm) cc_final: 0.7965 (mttm) REVERT: A 599 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7203 (mp) REVERT: A 622 MET cc_start: 0.5570 (ptp) cc_final: 0.5347 (ptp) REVERT: H 437 GLN cc_start: 0.7654 (mp10) cc_final: 0.7437 (mp10) REVERT: H 515 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7974 (mp) REVERT: H 526 SER cc_start: 0.7689 (p) cc_final: 0.7417 (t) REVERT: H 600 TYR cc_start: 0.7017 (t80) cc_final: 0.6756 (t80) REVERT: U 1 MET cc_start: 0.3675 (tpt) cc_final: 0.3393 (tpt) REVERT: C 83 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7691 (p-80) REVERT: D 105 MET cc_start: 0.6960 (mtt) cc_final: 0.6731 (mtp) outliers start: 48 outliers final: 39 residues processed: 270 average time/residue: 0.2223 time to fit residues: 88.3433 Evaluate side-chains 284 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 206 ILE 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 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 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 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 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 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 95 SER 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 G residue 7 ILE Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 91 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 25 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 116 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS H 161 HIS ** 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 = 0.4177 r_free = 0.4177 target = 0.165476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134510 restraints weight = 32093.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134865 restraints weight = 19089.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136284 restraints weight = 12766.397| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12792 Z= 0.110 Angle : 0.561 14.141 17439 Z= 0.278 Chirality : 0.038 0.189 2092 Planarity : 0.004 0.050 2224 Dihedral : 4.098 27.073 1809 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 3.96 % Allowed : 25.44 % 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: -0.20 (0.21), residues: 1678 helix: 1.18 (0.18), residues: 891 sheet: -0.60 (0.67), residues: 75 loop : -1.85 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 87 HIS 0.007 0.001 HIS H 334 PHE 0.025 0.001 PHE A 112 TYR 0.012 0.001 TYR D 79 ARG 0.007 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.00847 ( 2) hydrogen bonds : bond 0.04220 ( 511) hydrogen bonds : angle 3.71369 ( 1548) metal coordination : bond 0.00609 ( 11) metal coordination : angle 1.08154 ( 6) covalent geometry : bond 0.00246 (12778) covalent geometry : angle 0.56085 (17431) Misc. bond : bond 0.00021 ( 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 293 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8070 (mmp) cc_final: 0.7725 (mmp) REVERT: A 364 PHE cc_start: 0.7018 (m-80) cc_final: 0.6754 (m-80) REVERT: A 370 LYS cc_start: 0.8216 (mttm) cc_final: 0.8009 (mttm) REVERT: A 599 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7113 (mp) REVERT: A 622 MET cc_start: 0.5192 (ptp) cc_final: 0.4941 (ptp) REVERT: H 56 MET cc_start: 0.5205 (tpp) cc_final: 0.4003 (mmm) REVERT: H 515 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7956 (mp) REVERT: H 526 SER cc_start: 0.7699 (p) cc_final: 0.7420 (t) REVERT: H 600 TYR cc_start: 0.7008 (t80) cc_final: 0.6718 (t80) REVERT: U 1 MET cc_start: 0.3499 (tpt) cc_final: 0.3219 (tpt) REVERT: C 83 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7733 (p-80) REVERT: D 105 MET cc_start: 0.6955 (mtt) cc_final: 0.6705 (mtp) outliers start: 47 outliers final: 39 residues processed: 273 average time/residue: 0.2326 time to fit residues: 93.6497 Evaluate side-chains 286 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 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 395 CYS Chi-restraints excluded: chain A residue 519 LEU 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 235 HIS 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 336 ASP 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 95 SER 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 G residue 7 ILE 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: 0.8980 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 168 optimal weight: 0.0770 chunk 161 optimal weight: 0.0470 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 109 optimal weight: 0.0040 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 161 HIS H 226 HIS ** 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 = 0.4176 r_free = 0.4176 target = 0.165384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133240 restraints weight = 24610.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135271 restraints weight = 13229.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135534 restraints weight = 8353.429| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 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 = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12792 Z= 0.114 Angle : 0.576 14.282 17439 Z= 0.283 Chirality : 0.038 0.183 2092 Planarity : 0.005 0.050 2224 Dihedral : 4.086 27.080 1809 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 3.79 % Allowed : 25.61 % 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: -0.16 (0.21), residues: 1678 helix: 1.20 (0.18), residues: 893 sheet: -0.66 (0.67), residues: 75 loop : -1.82 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 14 HIS 0.006 0.001 HIS C 61 PHE 0.028 0.001 PHE A 112 TYR 0.012 0.001 TYR H 340 ARG 0.009 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00019 ( 1) link_TRANS : angle 0.00457 ( 2) hydrogen bonds : bond 0.04216 ( 511) hydrogen bonds : angle 3.72085 ( 1548) metal coordination : bond 0.00614 ( 11) metal coordination : angle 1.03380 ( 6) covalent geometry : bond 0.00256 (12778) covalent geometry : angle 0.57623 (17431) Misc. bond : bond 0.00021 ( 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 292 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.8039 (mmp) cc_final: 0.7702 (mmp) REVERT: A 364 PHE cc_start: 0.6935 (m-80) cc_final: 0.6689 (m-80) REVERT: A 370 LYS cc_start: 0.8134 (mttm) cc_final: 0.7915 (mttm) REVERT: A 517 TRP cc_start: 0.7700 (m100) cc_final: 0.6984 (m100) REVERT: A 599 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7315 (mp) REVERT: H 515 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7953 (mp) REVERT: H 526 SER cc_start: 0.7737 (p) cc_final: 0.7438 (t) REVERT: H 589 LEU cc_start: 0.8298 (mt) cc_final: 0.8082 (mp) REVERT: H 600 TYR cc_start: 0.6991 (t80) cc_final: 0.6710 (t80) REVERT: U 1 MET cc_start: 0.3860 (tpt) cc_final: 0.3615 (tpt) REVERT: C 83 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7710 (p-80) outliers start: 45 outliers final: 41 residues processed: 270 average time/residue: 0.2170 time to fit residues: 87.3140 Evaluate side-chains 288 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 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 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 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 336 ASP 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 95 SER 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 G residue 7 ILE 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 94 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 0.0070 chunk 124 optimal weight: 0.0670 chunk 163 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 91 optimal weight: 3.9990 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 161 HIS H 226 HIS ** 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 = 0.4186 r_free = 0.4186 target = 0.166207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136160 restraints weight = 39776.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135552 restraints weight = 22622.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137263 restraints weight = 16068.167| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12792 Z= 0.106 Angle : 0.568 14.382 17439 Z= 0.279 Chirality : 0.038 0.183 2092 Planarity : 0.004 0.050 2224 Dihedral : 3.998 26.572 1809 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 3.54 % Allowed : 26.28 % 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: -0.07 (0.21), residues: 1678 helix: 1.30 (0.18), residues: 890 sheet: -0.68 (0.66), residues: 75 loop : -1.78 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 14 HIS 0.007 0.001 HIS C 61 PHE 0.013 0.001 PHE A 202 TYR 0.012 0.001 TYR D 79 ARG 0.009 0.000 ARG H 424 Details of bonding type rmsd link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.00301 ( 2) hydrogen bonds : bond 0.03892 ( 511) hydrogen bonds : angle 3.65026 ( 1548) metal coordination : bond 0.00683 ( 11) metal coordination : angle 0.97038 ( 6) covalent geometry : bond 0.00237 (12778) covalent geometry : angle 0.56744 (17431) Misc. bond : bond 0.00018 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5473.87 seconds wall clock time: 96 minutes 0.73 seconds (5760.73 seconds total)