Starting phenix.real_space_refine on Thu Feb 5 13:14:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lu1_63386/02_2026/9lu1_63386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lu1_63386/02_2026/9lu1_63386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lu1_63386/02_2026/9lu1_63386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lu1_63386/02_2026/9lu1_63386.map" model { file = "/net/cci-nas-00/data/ceres_data/9lu1_63386/02_2026/9lu1_63386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lu1_63386/02_2026/9lu1_63386.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 10869 2.51 5 N 3061 2.21 5 O 3128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17116 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2049 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 312} Link IDs: {'PTRANS': 6, 'TRANS': 382} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1106 Unresolved non-hydrogen angles: 1403 Unresolved non-hydrogen dihedrals: 931 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'HIS:plan': 9, 'GLN:plan1': 12, 'GLU:plan': 25, 'PHE:plan': 15, 'ARG:plan': 17, 'ASN:plan1': 19, 'ASP:plan': 24, 'TYR:plan': 15, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 638 Chain: "B" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 404 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1054 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 136} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2278 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 7, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 743 Unresolved non-hydrogen angles: 927 Unresolved non-hydrogen dihedrals: 611 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU:plan': 22, 'PHE:plan': 8, 'ARG:plan': 16, 'ASN:plan1': 16, 'ASP:plan': 14, 'HIS:plan': 4, 'TYR:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 428 Chain: "R" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 13, 'GLN:plan1': 3, 'ASN:plan1': 6, 'ASP:plan': 12, 'HIS:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 206 Chain: "S" Number of atoms: 7294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 7294 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1055} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1357 Unresolved non-hydrogen angles: 1716 Unresolved non-hydrogen dihedrals: 1087 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLU:plan': 64, 'ASP:plan': 34, 'ARG:plan': 21, 'ASN:plan1': 17, 'GLN:plan1': 23, 'HIS:plan': 9, 'TRP:plan': 3, 'PHE:plan': 12, 'TYR:plan': 8} Unresolved non-hydrogen planarities: 806 Time building chain proxies: 2.93, per 1000 atoms: 0.17 Number of scatterers: 17116 At special positions: 0 Unit cell: (106.25, 144.5, 200.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 3128 8.00 N 3061 7.00 C 10869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 18 " - pdb=" SG CYS S 313 " distance=2.03 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 custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 874.9 milliseconds 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4892 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 46 sheets defined 16.3% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 257 through 301 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 60 through 66 Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.844A pdb=" N LYS C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 166 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.640A pdb=" N ALA C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'E' and resid 262 through 301 Processing helix chain 'E' and resid 357 through 371 removed outlier: 4.239A pdb=" N THR E 361 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP E 366 " --> pdb=" O ALA E 362 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 402 removed outlier: 3.554A pdb=" N PHE E 399 " --> pdb=" O CYS E 395 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 455 Processing helix chain 'R' and resid 17 through 28 removed outlier: 3.503A pdb=" N SER R 28 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 41 Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 110 through 124 removed outlier: 3.599A pdb=" N ASN R 115 " --> pdb=" O GLN R 111 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU R 122 " --> pdb=" O GLY R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 174 removed outlier: 3.533A pdb=" N VAL R 173 " --> pdb=" O PRO R 169 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 169 through 174' Processing helix chain 'R' and resid 216 through 220 Processing helix chain 'R' and resid 264 through 269 removed outlier: 3.658A pdb=" N SER R 269 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 309 Processing helix chain 'R' and resid 315 through 321 removed outlier: 4.025A pdb=" N PHE R 320 " --> pdb=" O LYS R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 removed outlier: 3.652A pdb=" N VAL R 352 " --> pdb=" O SER R 348 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR R 353 " --> pdb=" O GLU R 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 348 through 353' Processing helix chain 'R' and resid 384 through 393 Processing helix chain 'R' and resid 393 through 399 Processing helix chain 'R' and resid 417 through 431 removed outlier: 3.751A pdb=" N ILE R 421 " --> pdb=" O PHE R 417 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN R 422 " --> pdb=" O ALA R 418 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 446 removed outlier: 3.655A pdb=" N ALA R 440 " --> pdb=" O GLY R 436 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL R 441 " --> pdb=" O HIS R 437 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 384 Processing helix chain 'S' and resid 986 through 990 removed outlier: 3.675A pdb=" N GLN S 990 " --> pdb=" O GLU S 987 " (cutoff:3.500A) Processing helix chain 'S' and resid 1044 through 1060 removed outlier: 4.047A pdb=" N LYS S1060 " --> pdb=" O ASN S1056 " (cutoff:3.500A) Processing helix chain 'S' and resid 1069 through 1074 Processing helix chain 'S' and resid 1091 through 1096 Processing helix chain 'S' and resid 1097 through 1100 removed outlier: 3.559A pdb=" N ILE S1100 " --> pdb=" O PHE S1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1097 through 1100' Processing helix chain 'S' and resid 1101 through 1109 Processing helix chain 'S' and resid 1125 through 1137 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 412 removed outlier: 3.724A pdb=" N ARG A 406 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 729 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 727 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 410 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 725 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N THR A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 717 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 703 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA A 719 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 428 removed outlier: 4.466A pdb=" N SER A 426 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 439 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 440 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.599A pdb=" N ALA A 487 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 537 through 541 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 583 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 607 removed outlier: 3.619A pdb=" N TYR A 604 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 626 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS A 632 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 648 through 650 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 removed outlier: 5.913A pdb=" N LYS S 153 " --> pdb=" O PRO S 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE S 121 " --> pdb=" O ARG S 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'E' and resid 409 through 412 removed outlier: 3.574A pdb=" N ALA E 409 " --> pdb=" O VAL E 727 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR E 724 " --> pdb=" O ASN E 720 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 719 " --> pdb=" O ALA E 702 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA E 702 " --> pdb=" O ALA E 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 424 through 428 removed outlier: 7.131A pdb=" N ALA E 439 " --> pdb=" O SER E 425 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE E 427 " --> pdb=" O ALA E 437 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA E 437 " --> pdb=" O ILE E 427 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 476 through 478 removed outlier: 3.813A pdb=" N ALA E 487 " --> pdb=" O SER E 477 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 486 " --> pdb=" O TRP E 498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 516 through 521 removed outlier: 3.626A pdb=" N LEU E 529 " --> pdb=" O TRP E 541 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER E 533 " --> pdb=" O LYS E 537 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS E 537 " --> pdb=" O SER E 533 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 550 " --> pdb=" O LEU E 540 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 558 through 563 removed outlier: 4.117A pdb=" N CYS E 560 " --> pdb=" O GLY E 574 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS E 579 " --> pdb=" O CYS E 575 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 602 through 609 removed outlier: 4.433A pdb=" N TYR E 604 " --> pdb=" O ALA E 616 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU E 612 " --> pdb=" O VAL E 608 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 654 through 659 removed outlier: 3.552A pdb=" N ILE E 655 " --> pdb=" O TYR E 667 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS E 657 " --> pdb=" O TYR E 665 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 663 " --> pdb=" O SER E 659 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 50 through 53 removed outlier: 3.743A pdb=" N LEU R 517 " --> pdb=" O ARG R 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 61 through 65 removed outlier: 7.389A pdb=" N ILE R 73 " --> pdb=" O ARG R 63 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE R 65 " --> pdb=" O TYR R 71 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR R 71 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE R 72 " --> pdb=" O TYR R 85 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLU R 86 " --> pdb=" O LEU R 127 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU R 127 " --> pdb=" O GLU R 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 139 through 140 removed outlier: 6.581A pdb=" N GLU R 189 " --> pdb=" O CYS R 211 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS R 211 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 209 " --> pdb=" O TYR R 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP R 205 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASP R 197 " --> pdb=" O LEU R 203 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU R 203 " --> pdb=" O ASP R 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 222 through 225 removed outlier: 6.360A pdb=" N GLN R 243 " --> pdb=" O ASP R 252 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP R 252 " --> pdb=" O GLN R 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 330 through 338 removed outlier: 5.357A pdb=" N MET R 331 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N THR R 347 " --> pdb=" O MET R 331 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS R 333 " --> pdb=" O LYS R 345 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 377 " --> pdb=" O VAL R 367 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN R 369 " --> pdb=" O VAL R 375 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL R 375 " --> pdb=" O ASN R 369 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 466 through 467 removed outlier: 3.911A pdb=" N PHE R 499 " --> pdb=" O PHE R 489 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA R 491 " --> pdb=" O LEU R 497 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU R 497 " --> pdb=" O ALA R 491 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 4 through 10 removed outlier: 6.286A pdb=" N ILE S1037 " --> pdb=" O ALA S 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE S1030 " --> pdb=" O GLY S1038 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER S1042 " --> pdb=" O GLY S1026 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLY S1026 " --> pdb=" O SER S1042 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY S1031 " --> pdb=" O VAL S1006 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL S1006 " --> pdb=" O GLY S1031 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.547A pdb=" N GLY S 17 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS S 53 " --> pdb=" O ILE S 41 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL S 43 " --> pdb=" O PRO S 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 63 through 65 removed outlier: 6.721A pdb=" N ALA S 86 " --> pdb=" O HIS S 105 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS S 105 " --> pdb=" O ALA S 86 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE S 88 " --> pdb=" O ARG S 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 164 through 169 removed outlier: 4.099A pdb=" N ASP S 166 " --> pdb=" O VAL S 181 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL S 190 " --> pdb=" O TRP S 207 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N TRP S 207 " --> pdb=" O VAL S 190 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR S 192 " --> pdb=" O GLY S 205 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU S 201 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 216 through 222 removed outlier: 3.672A pdb=" N MET S 218 " --> pdb=" O ILE S 232 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY S 228 " --> pdb=" O VAL S 222 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN S 241 " --> pdb=" O LYS S 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 258 through 263 removed outlier: 3.644A pdb=" N GLY S 274 " --> pdb=" O CYS S 260 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG S 279 " --> pdb=" O ASP S 275 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU S 280 " --> pdb=" O LEU S 305 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP S 299 " --> pdb=" O GLU S 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 315 through 316 removed outlier: 3.515A pdb=" N THR S 315 " --> pdb=" O PHE S 323 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER S 331 " --> pdb=" O THR S 352 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR S 352 " --> pdb=" O SER S 331 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU S 333 " --> pdb=" O MET S 350 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 359 through 364 removed outlier: 3.896A pdb=" N ASP S 361 " --> pdb=" O CYS S 378 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY S 393 " --> pdb=" O LYS S 709 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS S 709 " --> pdb=" O GLY S 393 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 396 through 402 removed outlier: 5.337A pdb=" N GLU S 398 " --> pdb=" O THR S 703 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR S 703 " --> pdb=" O GLU S 398 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 411 through 413 Processing sheet with id=AD7, first strand: chain 'S' and resid 435 through 437 removed outlier: 3.852A pdb=" N VAL S 435 " --> pdb=" O THR S 446 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 457 through 460 removed outlier: 6.776A pdb=" N ILE S 471 " --> pdb=" O PHE S 458 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 467 through 468 Processing sheet with id=AE1, first strand: chain 'S' and resid 498 through 500 removed outlier: 7.131A pdb=" N ALA S 511 " --> pdb=" O SER S 499 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL S 508 " --> pdb=" O LEU S 519 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN S 520 " --> pdb=" O GLN S 528 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN S 528 " --> pdb=" O GLN S 520 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N HIS S 522 " --> pdb=" O LEU S 526 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU S 526 " --> pdb=" O HIS S 522 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 538 through 542 removed outlier: 6.954A pdb=" N GLY S 559 " --> pdb=" O ALA S 539 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU S 541 " --> pdb=" O ALA S 557 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA S 557 " --> pdb=" O LEU S 541 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 568 through 569 Processing sheet with id=AE4, first strand: chain 'S' and resid 590 through 595 Processing sheet with id=AE5, first strand: chain 'S' and resid 637 through 642 removed outlier: 9.131A pdb=" N THR S 647 " --> pdb=" O SER S 661 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER S 661 " --> pdb=" O THR S 647 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL S 649 " --> pdb=" O ILE S 659 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE S 659 " --> pdb=" O VAL S 649 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA S 651 " --> pdb=" O THR S 657 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR S 657 " --> pdb=" O ALA S 651 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 720 through 727 removed outlier: 3.637A pdb=" N SER S 720 " --> pdb=" O SER S 738 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU S 736 " --> pdb=" O ARG S 722 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE S 724 " --> pdb=" O GLY S 734 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY S 734 " --> pdb=" O ILE S 724 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR S 726 " --> pdb=" O CYS S 732 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N CYS S 732 " --> pdb=" O TYR S 726 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE S 794 " --> pdb=" O PHE S 733 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N HIS S 789 " --> pdb=" O GLN S 806 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN S 806 " --> pdb=" O HIS S 789 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU S 791 " --> pdb=" O ALA S 804 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA S 804 " --> pdb=" O LEU S 791 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE S 793 " --> pdb=" O LEU S 802 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER S 764 " --> pdb=" O GLN S 806 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 812 through 817 removed outlier: 5.303A pdb=" N ALA S 813 " --> pdb=" O ALA S 834 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA S 834 " --> pdb=" O ALA S 813 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER S 815 " --> pdb=" O GLY S 832 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA S 862 " --> pdb=" O VAL S 850 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN S 852 " --> pdb=" O THR S 860 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR S 860 " --> pdb=" O GLN S 852 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N SER S 854 " --> pdb=" O LEU S 858 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU S 858 " --> pdb=" O SER S 854 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 870 through 876 removed outlier: 4.831A pdb=" N SER S 872 " --> pdb=" O SER S 883 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU S 880 " --> pdb=" O TYR S 891 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU S 892 " --> pdb=" O THR S 901 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR S 901 " --> pdb=" O GLU S 892 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 913 through 917 removed outlier: 3.695A pdb=" N ALA S 946 " --> pdb=" O LEU S 932 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA S 934 " --> pdb=" O GLU S 944 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU S 944 " --> pdb=" O ALA S 934 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 954 through 959 removed outlier: 7.114A pdb=" N ALA S 968 " --> pdb=" O SER S 955 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL S 957 " --> pdb=" O LEU S 966 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU S 966 " --> pdb=" O VAL S 957 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS S 977 " --> pdb=" O PHE S 965 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN S 973 " --> pdb=" O GLU S 969 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY S 996 " --> pdb=" O VAL S 976 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN S 978 " --> pdb=" O GLU S 994 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU S 994 " --> pdb=" O GLN S 978 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1809 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: 4.57 Time building geometry restraints manager: 2.08 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: 5847 1.34 - 1.46: 3108 1.46 - 1.57: 8387 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 17423 Sorted by residual: bond pdb=" N ARG B 57 " pdb=" CA ARG B 57 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.27e-02 6.20e+03 1.28e+00 bond pdb=" C THR S 20 " pdb=" N GLY S 21 " ideal model delta sigma weight residual 1.329 1.320 0.009 9.60e-03 1.09e+04 8.18e-01 bond pdb=" CG PRO S 225 " pdb=" CD PRO S 225 " ideal model delta sigma weight residual 1.512 1.493 0.019 2.70e-02 1.37e+03 4.89e-01 bond pdb=" C SER R 464 " pdb=" N LEU R 465 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.73e-02 3.34e+03 4.85e-01 bond pdb=" C GLY S 21 " pdb=" O GLY S 21 " ideal model delta sigma weight residual 1.232 1.223 0.009 1.31e-02 5.83e+03 4.80e-01 ... (remaining 17418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 23765 2.60 - 5.20: 125 5.20 - 7.80: 11 7.80 - 10.40: 0 10.40 - 13.00: 1 Bond angle restraints: 23902 Sorted by residual: angle pdb=" N MET R 314 " pdb=" CA MET R 314 " pdb=" C MET R 314 " ideal model delta sigma weight residual 114.56 108.66 5.90 1.27e+00 6.20e-01 2.15e+01 angle pdb=" CA LEU R 354 " pdb=" CB LEU R 354 " pdb=" CG LEU R 354 " ideal model delta sigma weight residual 116.30 129.30 -13.00 3.50e+00 8.16e-02 1.38e+01 angle pdb=" N VAL R 133 " pdb=" CA VAL R 133 " pdb=" C VAL R 133 " ideal model delta sigma weight residual 113.47 110.28 3.19 1.01e+00 9.80e-01 9.99e+00 angle pdb=" N GLY A 723 " pdb=" CA GLY A 723 " pdb=" C GLY A 723 " ideal model delta sigma weight residual 113.18 120.58 -7.40 2.37e+00 1.78e-01 9.74e+00 angle pdb=" CA MET R 314 " pdb=" C MET R 314 " pdb=" N ALA R 315 " ideal model delta sigma weight residual 119.26 116.04 3.22 1.14e+00 7.69e-01 7.96e+00 ... (remaining 23897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 9193 17.63 - 35.26: 763 35.26 - 52.90: 205 52.90 - 70.53: 31 70.53 - 88.16: 10 Dihedral angle restraints: 10202 sinusoidal: 2679 harmonic: 7523 Sorted by residual: dihedral pdb=" CA GLU R 165 " pdb=" C GLU R 165 " pdb=" N PRO R 166 " pdb=" CA PRO R 166 " ideal model delta harmonic sigma weight residual 180.00 140.32 39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA GLU S1079 " pdb=" C GLU S1079 " pdb=" N ARG S1080 " pdb=" CA ARG S1080 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP R 164 " pdb=" C ASP R 164 " pdb=" N GLU R 165 " pdb=" CA GLU R 165 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 10199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1754 0.030 - 0.060: 736 0.060 - 0.090: 235 0.090 - 0.120: 169 0.120 - 0.150: 19 Chirality restraints: 2913 Sorted by residual: chirality pdb=" CA VAL S 212 " pdb=" N VAL S 212 " pdb=" C VAL S 212 " pdb=" CB VAL S 212 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE E 438 " pdb=" N ILE E 438 " pdb=" C ILE E 438 " pdb=" CB ILE E 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE S 848 " pdb=" N ILE S 848 " pdb=" C ILE S 848 " pdb=" CB ILE S 848 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 2910 not shown) Planarity restraints: 3149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU R 165 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO R 166 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 272 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO R 273 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 273 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 273 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 184 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO S 185 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO S 185 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 185 " 0.025 5.00e-02 4.00e+02 ... (remaining 3146 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 357 2.68 - 3.23: 15170 3.23 - 3.79: 24083 3.79 - 4.34: 29100 4.34 - 4.90: 51355 Nonbonded interactions: 120065 Sorted by model distance: nonbonded pdb=" OD2 ASP S 824 " pdb=" OH TYR S 828 " model vdw 2.122 3.040 nonbonded pdb=" OE1 GLN S 209 " pdb=" N GLU S 210 " model vdw 2.165 3.120 nonbonded pdb=" OG1 THR R 372 " pdb=" OE2 GLU R 374 " model vdw 2.195 3.040 nonbonded pdb=" N GLU E 513 " pdb=" OE1 GLU E 513 " model vdw 2.203 3.120 nonbonded pdb=" O LYS E 637 " pdb=" OH TYR E 667 " model vdw 2.211 3.040 ... (remaining 120060 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 261 through 301 or (resid 356 through 373 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 389 through 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 or (resid 408 through 4 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 413 through \ 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or r \ esid 423 through 455 or (resid 460 through 462 and (name N or name CA or name C \ or name O or name CB )) or resid 463 through 477 or (resid 478 through 492 and ( \ name N or name CA or name C or name O or name CB )) or resid 493 through 679 or \ (resid 680 and (name N or name CA or name C or name O or name CB )) or resid 683 \ or resid 686 or (resid 713 through 722 and (name N or name CA or name C or name \ O or name CB )) or resid 723 or (resid 724 and (name N or name CA or name C or \ name O or name CB )) or resid 725 through 726 or (resid 727 through 728 and (nam \ e N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 261 through 373 and (name N or name CA or name C or name \ O or name CB )) or resid 389 through 425 or (resid 426 through 428 and (name N o \ r name CA or name C or name O or name CB )) or resid 429 through 431 or (resid 4 \ 32 through 439 and (name N or name CA or name C or name O or name CB )) or (resi \ d 440 through 449 and (name N or name CA or name C or name O or name CB )) or re \ sid 450 through 466 or (resid 467 through 475 and (name N or name CA or name C o \ r name O or name CB )) or resid 476 through 481 or (resid 482 through 492 and (n \ ame N or name CA or name C or name O or name CB )) or resid 493 or (resid 494 th \ rough 499 and (name N or name CA or name C or name O or name CB )) or resid 500 \ through 504 or (resid 505 and (name N or name CA or name C or name O or name CB \ )) or (resid 515 through 525 and (name N or name CA or name C or name O or name \ CB )) or resid 526 through 527 or (resid 528 through 531 and (name N or name CA \ or name C or name O or name CB )) or resid 532 or (resid 533 through 564 and (na \ me N or name CA or name C or name O or name CB )) or resid 565 through 566 or (r \ esid 567 through 573 and (name N or name CA or name C or name O or name CB )) or \ resid 574 or (resid 575 through 596 and (name N or name CA or name C or name O \ or name CB )) or (resid 597 through 609 and (name N or name CA or name C or name \ O or name CB )) or (resid 610 through 627 and (name N or name CA or name C or n \ ame O or name CB )) or resid 628 through 644 or (resid 645 through 646 and (name \ N or name CA or name C or name O or name CB )) or resid 647 or (resid 648 throu \ gh 651 and (name N or name CA or name C or name O or name CB )) or (resid 652 th \ rough 657 and (name N or name CA or name C or name O or name CB )) or (resid 658 \ through 669 and (name N or name CA or name C or name O or name CB )) or (resid \ 670 through 680 and (name N or name CA or name C or name O or name CB )) or (res \ id 700 and (name N or name CA or name C or name O or name CB )) or (resid 703 an \ d (name N or name CA or name C or name O or name CB )) or (resid 713 through 722 \ and (name N or name CA or name C or name O or name CB )) or resid 723 through 7 \ 28)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.020 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.590 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.003 0.029 17424 Z= 0.130 Angle : 0.520 12.995 23904 Z= 0.282 Chirality : 0.042 0.150 2913 Planarity : 0.003 0.047 3149 Dihedral : 15.079 88.161 5307 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.96 % Favored : 93.68 % Rotamer: Outliers : 0.16 % Allowed : 29.06 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 2533 helix: 1.97 (0.28), residues: 394 sheet: -0.77 (0.18), residues: 837 loop : -1.83 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 355 TYR 0.013 0.001 TYR A 450 PHE 0.010 0.001 PHE R 242 TRP 0.011 0.001 TRP S 953 HIS 0.003 0.001 HIS E 512 Details of bonding type rmsd covalent geometry : bond 0.00280 (17423) covalent geometry : angle 0.52010 (23902) SS BOND : bond 0.00113 ( 1) SS BOND : angle 1.27394 ( 2) hydrogen bonds : bond 0.12987 ( 658) hydrogen bonds : angle 5.73025 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: E 513 GLU cc_start: 0.8638 (pm20) cc_final: 0.8355 (pm20) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.1028 time to fit residues: 12.0299 Evaluate side-chains 62 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 209 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0060 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 GLN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.063440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046997 restraints weight = 97676.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048208 restraints weight = 48216.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049001 restraints weight = 30102.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049545 restraints weight = 21743.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049904 restraints weight = 17274.123| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17424 Z= 0.253 Angle : 0.592 6.748 23904 Z= 0.317 Chirality : 0.045 0.153 2913 Planarity : 0.004 0.051 3149 Dihedral : 4.618 55.279 2703 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.29 % Favored : 91.43 % Rotamer: Outliers : 4.38 % Allowed : 26.04 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2533 helix: 1.78 (0.28), residues: 393 sheet: -0.86 (0.18), residues: 822 loop : -1.93 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 134 TYR 0.015 0.001 TYR E 604 PHE 0.018 0.002 PHE R 393 TRP 0.017 0.001 TRP S 953 HIS 0.007 0.001 HIS R 218 Details of bonding type rmsd covalent geometry : bond 0.00574 (17423) covalent geometry : angle 0.59163 (23902) SS BOND : bond 0.00137 ( 1) SS BOND : angle 1.96367 ( 2) hydrogen bonds : bond 0.04059 ( 658) hydrogen bonds : angle 5.12716 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 61 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 513 GLU cc_start: 0.8868 (pm20) cc_final: 0.8505 (pm20) REVERT: S 3 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: S 109 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: S 350 MET cc_start: 0.8574 (ptp) cc_final: 0.8362 (ptp) outliers start: 55 outliers final: 25 residues processed: 112 average time/residue: 0.0945 time to fit residues: 18.2155 Evaluate side-chains 86 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 705 TRP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 344 ILE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 109 GLN Chi-restraints excluded: chain S residue 124 ILE Chi-restraints excluded: chain S residue 226 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 930 VAL Chi-restraints excluded: chain S residue 931 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 137 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 229 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 16 GLN S 22 HIS ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1055 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048128 restraints weight = 97341.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049376 restraints weight = 47383.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050177 restraints weight = 29344.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050750 restraints weight = 21119.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051096 restraints weight = 16712.978| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17424 Z= 0.126 Angle : 0.501 8.243 23904 Z= 0.266 Chirality : 0.043 0.150 2913 Planarity : 0.003 0.054 3149 Dihedral : 4.087 45.709 2700 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 3.42 % Allowed : 27.23 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2533 helix: 2.02 (0.28), residues: 393 sheet: -0.78 (0.18), residues: 829 loop : -1.83 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 355 TYR 0.013 0.001 TYR E 604 PHE 0.009 0.001 PHE R 242 TRP 0.011 0.001 TRP E 498 HIS 0.003 0.001 HIS R 547 Details of bonding type rmsd covalent geometry : bond 0.00283 (17423) covalent geometry : angle 0.50082 (23902) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.12145 ( 2) hydrogen bonds : bond 0.03162 ( 658) hydrogen bonds : angle 4.72310 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.4330 (m-80) REVERT: E 513 GLU cc_start: 0.8807 (pm20) cc_final: 0.8501 (pm20) REVERT: S 3 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: S 109 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (pm20) REVERT: S 134 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.6897 (tmm160) outliers start: 43 outliers final: 18 residues processed: 104 average time/residue: 0.1105 time to fit residues: 19.3543 Evaluate side-chains 82 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 109 GLN Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 322 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 1029 LEU Chi-restraints excluded: chain S residue 1071 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 250 optimal weight: 0.3980 chunk 50 optimal weight: 0.0970 chunk 168 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 217 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.065030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048626 restraints weight = 96965.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.049888 restraints weight = 46905.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050723 restraints weight = 28948.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051280 restraints weight = 20697.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051620 restraints weight = 16368.471| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17424 Z= 0.098 Angle : 0.487 8.044 23904 Z= 0.256 Chirality : 0.043 0.158 2913 Planarity : 0.003 0.056 3149 Dihedral : 3.884 41.164 2700 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.51 % Favored : 93.29 % Rotamer: Outliers : 3.66 % Allowed : 27.23 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2533 helix: 2.15 (0.28), residues: 393 sheet: -0.72 (0.18), residues: 828 loop : -1.77 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 134 TYR 0.008 0.001 TYR R 191 PHE 0.009 0.001 PHE S 975 TRP 0.009 0.001 TRP E 625 HIS 0.003 0.000 HIS R 547 Details of bonding type rmsd covalent geometry : bond 0.00220 (17423) covalent geometry : angle 0.48695 (23902) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.88570 ( 2) hydrogen bonds : bond 0.02829 ( 658) hydrogen bonds : angle 4.50531 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: E 513 GLU cc_start: 0.8863 (pm20) cc_final: 0.8591 (pm20) REVERT: S 3 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: S 134 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7032 (tmm-80) outliers start: 46 outliers final: 25 residues processed: 108 average time/residue: 0.1142 time to fit residues: 20.7973 Evaluate side-chains 88 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 705 TRP Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 322 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 1029 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 12 optimal weight: 30.0000 chunk 134 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 165 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.065772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049453 restraints weight = 95141.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050740 restraints weight = 46149.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051577 restraints weight = 28357.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052149 restraints weight = 20257.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.052546 restraints weight = 15999.688| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17424 Z= 0.080 Angle : 0.469 8.178 23904 Z= 0.245 Chirality : 0.043 0.155 2913 Planarity : 0.003 0.056 3149 Dihedral : 3.654 39.040 2700 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 2.87 % Allowed : 27.63 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2533 helix: 2.20 (0.28), residues: 399 sheet: -0.59 (0.18), residues: 836 loop : -1.70 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 398 TYR 0.008 0.001 TYR R 191 PHE 0.014 0.001 PHE R 417 TRP 0.008 0.001 TRP E 541 HIS 0.004 0.000 HIS R 547 Details of bonding type rmsd covalent geometry : bond 0.00177 (17423) covalent geometry : angle 0.46947 (23902) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.69255 ( 2) hydrogen bonds : bond 0.02538 ( 658) hydrogen bonds : angle 4.28149 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: E 473 ILE cc_start: 0.8694 (mm) cc_final: 0.7856 (tp) REVERT: E 513 GLU cc_start: 0.8955 (pm20) cc_final: 0.8659 (pm20) REVERT: S 3 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7651 (m-80) outliers start: 36 outliers final: 21 residues processed: 100 average time/residue: 0.0997 time to fit residues: 17.9326 Evaluate side-chains 86 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 322 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 1029 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 237 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 241 optimal weight: 1.9990 chunk 71 optimal weight: 0.0030 chunk 128 optimal weight: 6.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.065190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048766 restraints weight = 95945.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050041 restraints weight = 45703.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.050889 restraints weight = 28049.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051447 restraints weight = 20016.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.051829 restraints weight = 15823.138| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17424 Z= 0.121 Angle : 0.483 8.045 23904 Z= 0.253 Chirality : 0.043 0.176 2913 Planarity : 0.003 0.054 3149 Dihedral : 3.700 38.934 2700 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.63 % Favored : 93.21 % Rotamer: Outliers : 3.82 % Allowed : 26.99 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.17), residues: 2533 helix: 2.24 (0.28), residues: 399 sheet: -0.58 (0.19), residues: 826 loop : -1.69 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 134 TYR 0.011 0.001 TYR E 604 PHE 0.011 0.001 PHE R 417 TRP 0.008 0.001 TRP E 541 HIS 0.002 0.001 HIS R 341 Details of bonding type rmsd covalent geometry : bond 0.00275 (17423) covalent geometry : angle 0.48337 (23902) SS BOND : bond 0.00117 ( 1) SS BOND : angle 1.03114 ( 2) hydrogen bonds : bond 0.02784 ( 658) hydrogen bonds : angle 4.31394 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 62 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.4341 (m-80) REVERT: E 473 ILE cc_start: 0.8842 (mm) cc_final: 0.8566 (mm) REVERT: E 513 GLU cc_start: 0.8948 (pm20) cc_final: 0.8677 (pm20) REVERT: R 128 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8950 (mm) REVERT: S 3 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: S 134 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6992 (tmm-80) outliers start: 48 outliers final: 35 residues processed: 106 average time/residue: 0.0976 time to fit residues: 18.2010 Evaluate side-chains 101 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 705 TRP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 344 ILE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 322 VAL Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 927 MET Chi-restraints excluded: chain S residue 1029 LEU Chi-restraints excluded: chain S residue 1086 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 28 optimal weight: 20.0000 chunk 134 optimal weight: 0.7980 chunk 20 optimal weight: 50.0000 chunk 144 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.065600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049190 restraints weight = 96280.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050486 restraints weight = 45627.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051349 restraints weight = 27862.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051935 restraints weight = 19770.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052273 restraints weight = 15501.909| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17424 Z= 0.094 Angle : 0.471 8.066 23904 Z= 0.245 Chirality : 0.043 0.185 2913 Planarity : 0.003 0.054 3149 Dihedral : 3.613 38.328 2700 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 3.58 % Allowed : 27.39 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.17), residues: 2533 helix: 2.41 (0.28), residues: 389 sheet: -0.51 (0.19), residues: 836 loop : -1.69 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 134 TYR 0.011 0.001 TYR E 604 PHE 0.010 0.001 PHE R 417 TRP 0.007 0.001 TRP E 541 HIS 0.003 0.000 HIS R 547 Details of bonding type rmsd covalent geometry : bond 0.00214 (17423) covalent geometry : angle 0.47091 (23902) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.88876 ( 2) hydrogen bonds : bond 0.02596 ( 658) hydrogen bonds : angle 4.22292 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.4423 (m-80) REVERT: E 473 ILE cc_start: 0.8869 (mm) cc_final: 0.8620 (mm) REVERT: E 513 GLU cc_start: 0.8934 (pm20) cc_final: 0.8730 (pm20) REVERT: R 128 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8938 (mm) REVERT: R 395 ASP cc_start: 0.9260 (t0) cc_final: 0.8997 (p0) REVERT: S 3 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: S 134 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.6985 (tmm-80) outliers start: 45 outliers final: 33 residues processed: 106 average time/residue: 0.1104 time to fit residues: 19.8778 Evaluate side-chains 100 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 322 VAL Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 1029 LEU Chi-restraints excluded: chain S residue 1086 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 166 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 129 optimal weight: 0.0370 chunk 104 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.065282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048909 restraints weight = 96644.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050197 restraints weight = 45826.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051041 restraints weight = 27980.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051620 restraints weight = 19920.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051954 restraints weight = 15698.766| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17424 Z= 0.112 Angle : 0.478 8.010 23904 Z= 0.249 Chirality : 0.043 0.182 2913 Planarity : 0.003 0.052 3149 Dihedral : 3.626 38.551 2700 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.63 % Favored : 93.21 % Rotamer: Outliers : 3.74 % Allowed : 27.47 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2533 helix: 2.44 (0.28), residues: 389 sheet: -0.50 (0.19), residues: 836 loop : -1.67 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 134 TYR 0.012 0.001 TYR E 604 PHE 0.011 0.001 PHE R 417 TRP 0.008 0.001 TRP E 541 HIS 0.002 0.001 HIS R 341 Details of bonding type rmsd covalent geometry : bond 0.00255 (17423) covalent geometry : angle 0.47833 (23902) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.99246 ( 2) hydrogen bonds : bond 0.02690 ( 658) hydrogen bonds : angle 4.22484 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.4389 (m-80) REVERT: E 473 ILE cc_start: 0.8934 (mm) cc_final: 0.8681 (mm) REVERT: E 513 GLU cc_start: 0.8922 (pm20) cc_final: 0.8701 (pm20) REVERT: R 128 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8927 (mm) REVERT: R 395 ASP cc_start: 0.9268 (t0) cc_final: 0.8997 (p0) REVERT: S 3 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: S 134 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.6954 (tmm-80) REVERT: S 969 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8622 (pp20) outliers start: 47 outliers final: 35 residues processed: 109 average time/residue: 0.0997 time to fit residues: 18.7618 Evaluate side-chains 104 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 64 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 705 TRP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 344 ILE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 322 VAL Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 969 GLU Chi-restraints excluded: chain S residue 1029 LEU Chi-restraints excluded: chain S residue 1086 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 210 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 0.4980 chunk 24 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.063625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047185 restraints weight = 97594.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048418 restraints weight = 47074.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049237 restraints weight = 29063.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.049774 restraints weight = 20875.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050102 restraints weight = 16584.402| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17424 Z= 0.216 Angle : 0.558 7.908 23904 Z= 0.294 Chirality : 0.044 0.199 2913 Planarity : 0.003 0.048 3149 Dihedral : 4.083 40.004 2700 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.29 % Favored : 91.55 % Rotamer: Outliers : 3.58 % Allowed : 27.47 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.17), residues: 2533 helix: 2.04 (0.28), residues: 400 sheet: -0.58 (0.19), residues: 837 loop : -1.76 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 134 TYR 0.012 0.001 TYR S 316 PHE 0.016 0.001 PHE R 242 TRP 0.011 0.001 TRP E 541 HIS 0.004 0.001 HIS R 403 Details of bonding type rmsd covalent geometry : bond 0.00491 (17423) covalent geometry : angle 0.55826 (23902) SS BOND : bond 0.00207 ( 1) SS BOND : angle 1.53644 ( 2) hydrogen bonds : bond 0.03500 ( 658) hydrogen bonds : angle 4.62669 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 62 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.4489 (m-80) REVERT: E 473 ILE cc_start: 0.9191 (mm) cc_final: 0.8920 (mm) REVERT: R 128 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8914 (mm) REVERT: R 395 ASP cc_start: 0.9294 (t0) cc_final: 0.9021 (p0) REVERT: S 3 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: S 969 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8723 (pp20) outliers start: 45 outliers final: 35 residues processed: 103 average time/residue: 0.1000 time to fit residues: 17.4121 Evaluate side-chains 100 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 705 TRP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 344 ILE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 226 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 816 LEU Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 969 GLU Chi-restraints excluded: chain S residue 1086 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 198 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.063625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047209 restraints weight = 96603.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048427 restraints weight = 47084.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049237 restraints weight = 29259.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049762 restraints weight = 21122.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050154 restraints weight = 16859.902| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17424 Z= 0.200 Angle : 0.549 8.095 23904 Z= 0.289 Chirality : 0.044 0.205 2913 Planarity : 0.003 0.049 3149 Dihedral : 4.119 40.946 2700 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.26 % Favored : 92.58 % Rotamer: Outliers : 3.34 % Allowed : 27.71 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2533 helix: 2.07 (0.28), residues: 394 sheet: -0.64 (0.19), residues: 824 loop : -1.80 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 134 TYR 0.010 0.001 TYR S 812 PHE 0.014 0.001 PHE R 417 TRP 0.045 0.002 TRP E 625 HIS 0.003 0.001 HIS R 403 Details of bonding type rmsd covalent geometry : bond 0.00458 (17423) covalent geometry : angle 0.54905 (23902) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.63163 ( 2) hydrogen bonds : bond 0.03316 ( 658) hydrogen bonds : angle 4.63773 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5066 Ramachandran restraints generated. 2533 Oldfield, 0 Emsley, 2533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 62 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.4477 (m-80) REVERT: E 473 ILE cc_start: 0.9228 (mm) cc_final: 0.8976 (mm) REVERT: R 128 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8878 (mm) REVERT: S 3 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: S 969 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8701 (pp20) outliers start: 42 outliers final: 37 residues processed: 100 average time/residue: 0.1023 time to fit residues: 17.3665 Evaluate side-chains 101 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 705 TRP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 153 CYS Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 344 ILE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 402 LEU Chi-restraints excluded: chain S residue 3 TYR Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 226 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 725 CYS Chi-restraints excluded: chain S residue 742 VAL Chi-restraints excluded: chain S residue 816 LEU Chi-restraints excluded: chain S residue 817 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 921 ILE Chi-restraints excluded: chain S residue 969 GLU Chi-restraints excluded: chain S residue 1086 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 149 optimal weight: 0.1980 chunk 128 optimal weight: 0.1980 chunk 181 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 125 optimal weight: 0.1980 chunk 141 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.065676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049352 restraints weight = 95180.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050642 restraints weight = 45416.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051500 restraints weight = 27782.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052066 restraints weight = 19767.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.052460 restraints weight = 15650.137| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17424 Z= 0.078 Angle : 0.488 10.805 23904 Z= 0.251 Chirality : 0.043 0.181 2913 Planarity : 0.003 0.055 3149 Dihedral : 3.696 39.195 2700 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 2.39 % Allowed : 28.90 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.17), residues: 2533 helix: 2.34 (0.28), residues: 390 sheet: -0.51 (0.19), residues: 842 loop : -1.67 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 38 TYR 0.008 0.001 TYR R 191 PHE 0.012 0.001 PHE E 595 TRP 0.019 0.001 TRP E 625 HIS 0.003 0.000 HIS R 547 Details of bonding type rmsd covalent geometry : bond 0.00170 (17423) covalent geometry : angle 0.48815 (23902) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.60793 ( 2) hydrogen bonds : bond 0.02477 ( 658) hydrogen bonds : angle 4.29112 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3362.41 seconds wall clock time: 58 minutes 28.60 seconds (3508.60 seconds total)