Starting phenix.real_space_refine on Wed Jun 11 11:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ttu_10585/06_2025/6ttu_10585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ttu_10585/06_2025/6ttu_10585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ttu_10585/06_2025/6ttu_10585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ttu_10585/06_2025/6ttu_10585.map" model { file = "/net/cci-nas-00/data/ceres_data/6ttu_10585/06_2025/6ttu_10585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ttu_10585/06_2025/6ttu_10585.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1 5.49 5 S 69 5.16 5 C 8099 2.51 5 N 2204 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12746 Number of models: 1 Model: "" Number of chains: 9 Chain: "T" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3085 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 891 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5728 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 688} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 666 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "D" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1135 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 58 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10515 SG CYS R 42 72.537 59.783 38.458 1.00105.69 S ATOM 10534 SG CYS R 45 71.727 62.144 41.587 1.00 96.79 S ATOM 10782 SG CYS R 83 74.603 62.879 39.323 1.00114.58 S ATOM 10711 SG CYS R 75 77.674 50.473 29.345 1.00132.51 S ATOM 10878 SG CYS R 94 78.374 51.519 33.079 1.00107.60 S ATOM 10601 SG CYS R 53 73.307 67.468 39.926 1.00145.22 S ATOM 10624 SG CYS R 56 72.428 70.984 38.455 1.00149.84 S ATOM 10661 SG CYS R 68 71.603 67.584 36.570 1.00150.04 S Time building chain proxies: 7.51, per 1000 atoms: 0.59 Number of scatterers: 12746 At special positions: 0 Unit cell: (129.32, 87.98, 163.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 69 16.00 P 1 15.00 O 2370 8.00 N 2204 7.00 C 8099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS T 298 " - pdb=" SG CYS T 335 " distance=2.05 Simple disulfide: pdb=" SG CYS D 85 " - pdb=" SG CYS I 20 " distance=2.01 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=1, symmetry=0 Links applied TRANS " CYS I 20 " - " GLY U 75 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 6 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 15 sheets defined 50.3% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'T' and resid 179 through 187 Proline residue: T 185 - end of helix Processing helix chain 'T' and resid 189 through 199 removed outlier: 3.724A pdb=" N TYR T 199 " --> pdb=" O ASN T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 210 Processing helix chain 'T' and resid 212 through 222 Processing helix chain 'T' and resid 223 through 236 Processing helix chain 'T' and resid 236 through 247 Processing helix chain 'T' and resid 248 through 252 Processing helix chain 'T' and resid 265 through 289 removed outlier: 3.929A pdb=" N ARG T 269 " --> pdb=" O ASN T 265 " (cutoff:3.500A) Proline residue: T 273 - end of helix Processing helix chain 'T' and resid 533 through 538 removed outlier: 3.697A pdb=" N ASP T 538 " --> pdb=" O VAL T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 542 through 545 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 31 Processing helix chain 'S' and resid 45 through 59 Processing helix chain 'S' and resid 69 through 76 Processing helix chain 'S' and resid 78 through 93 Processing helix chain 'S' and resid 94 through 108 Processing helix chain 'S' and resid 113 through 122 Processing helix chain 'S' and resid 131 through 138 Processing helix chain 'C' and resid 17 through 33 removed outlier: 3.846A pdb=" N THR C 33 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.781A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 Processing helix chain 'C' and resid 113 through 137 removed outlier: 3.827A pdb=" N LYS C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.024A pdb=" N VAL C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.880A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 252 removed outlier: 3.901A pdb=" N SER C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 278 removed outlier: 3.555A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 4.563A pdb=" N GLU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.747A pdb=" N GLN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.840A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 354 removed outlier: 3.575A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.921A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.973A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.737A pdb=" N LYS C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.624A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.601A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 525 removed outlier: 7.165A pdb=" N PHE C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 Processing helix chain 'C' and resid 604 through 614 Processing helix chain 'C' and resid 622 through 627 Processing helix chain 'C' and resid 632 through 645 removed outlier: 4.539A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 723 removed outlier: 4.431A pdb=" N LYS C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'N' and resid 22 through 32 removed outlier: 3.547A pdb=" N VAL N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 removed outlier: 3.627A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.758A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 112 removed outlier: 3.640A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 4.276A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.604A pdb=" N ARG D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 37 through 41 Processing helix chain 'U' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'T' and resid 308 through 311 removed outlier: 3.972A pdb=" N CYS T 308 " --> pdb=" O GLY T 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP T 329 " --> pdb=" O CYS T 335 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS T 335 " --> pdb=" O ASP T 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 346 through 351 removed outlier: 6.604A pdb=" N ASP T 369 " --> pdb=" O MET T 375 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET T 375 " --> pdb=" O ASP T 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 386 through 392 removed outlier: 6.396A pdb=" N ILE T 405 " --> pdb=" O VAL T 421 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL T 421 " --> pdb=" O ILE T 405 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL T 407 " --> pdb=" O ARG T 419 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP T 415 " --> pdb=" O ALA T 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 429 through 434 removed outlier: 3.806A pdb=" N SER T 443 " --> pdb=" O THR T 447 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR T 447 " --> pdb=" O SER T 443 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASN T 452 " --> pdb=" O PHE T 458 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE T 458 " --> pdb=" O ASN T 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 469 through 475 removed outlier: 3.666A pdb=" N ARG T 500 " --> pdb=" O LEU T 490 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP T 492 " --> pdb=" O CYS T 498 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N CYS T 498 " --> pdb=" O ASP T 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 509 through 514 removed outlier: 6.809A pdb=" N ASP T 532 " --> pdb=" O CYS T 547 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS T 547 " --> pdb=" O ASP T 532 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 560 through 563 Processing sheet with id=AA8, first strand: chain 'S' and resid 13 through 17 removed outlier: 9.556A pdb=" N VAL S 39 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LYS S 5 " --> pdb=" O VAL S 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 534 through 541 removed outlier: 3.661A pdb=" N ALA R 29 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 31 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU R 32 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 599 through 602 removed outlier: 3.573A pdb=" N VAL C 591 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU R 23 " --> pdb=" O VAL C 591 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 620 through 621 removed outlier: 3.902A pdb=" N TYR C 620 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 12 through 17 removed outlier: 8.689A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL N 70 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.599A pdb=" N SER D 22 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 35 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 12 through 16 664 hydrogen bonds defined for protein. 1920 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: 4.01 Time building geometry restraints manager: 3.70 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: 4182 1.34 - 1.47: 3008 1.47 - 1.60: 5682 1.60 - 1.72: 1 1.72 - 1.85: 99 Bond restraints: 12972 Sorted by residual: bond pdb=" O3P SEP I 32 " pdb=" P SEP I 32 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1P SEP I 32 " pdb=" P SEP I 32 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" O2P SEP I 32 " pdb=" P SEP I 32 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CA VAL C 746 " pdb=" CB VAL C 746 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.41e+01 bond pdb=" C LEU D 89 " pdb=" N ARG D 90 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.25e-02 6.40e+03 1.04e+01 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16878 2.04 - 4.08: 581 4.08 - 6.12: 63 6.12 - 8.16: 13 8.16 - 10.20: 7 Bond angle restraints: 17542 Sorted by residual: angle pdb=" N LYS S 110 " pdb=" CA LYS S 110 " pdb=" C LYS S 110 " ideal model delta sigma weight residual 110.24 119.55 -9.31 1.30e+00 5.92e-01 5.13e+01 angle pdb=" C TYR C 583 " pdb=" N GLN C 584 " pdb=" CA GLN C 584 " ideal model delta sigma weight residual 122.31 112.59 9.72 2.00e+00 2.50e-01 2.36e+01 angle pdb=" N CYS C 170 " pdb=" CA CYS C 170 " pdb=" C CYS C 170 " ideal model delta sigma weight residual 113.72 107.41 6.31 1.30e+00 5.92e-01 2.36e+01 angle pdb=" N GLU C 763 " pdb=" CA GLU C 763 " pdb=" C GLU C 763 " ideal model delta sigma weight residual 108.34 114.59 -6.25 1.31e+00 5.83e-01 2.27e+01 angle pdb=" N LYS C 189 " pdb=" CA LYS C 189 " pdb=" C LYS C 189 " ideal model delta sigma weight residual 112.38 107.05 5.33 1.22e+00 6.72e-01 1.91e+01 ... (remaining 17537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6998 17.93 - 35.85: 673 35.85 - 53.78: 137 53.78 - 71.71: 32 71.71 - 89.63: 14 Dihedral angle restraints: 7854 sinusoidal: 3148 harmonic: 4706 Sorted by residual: dihedral pdb=" CB CYS D 85 " pdb=" SG CYS D 85 " pdb=" SG CYS I 20 " pdb=" CB CYS I 20 " ideal model delta sinusoidal sigma weight residual -86.00 -20.18 -65.82 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA ASP C 362 " pdb=" CB ASP C 362 " pdb=" CG ASP C 362 " pdb=" OD1 ASP C 362 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 239 " pdb=" CB ASP C 239 " pdb=" CG ASP C 239 " pdb=" OD1 ASP C 239 " ideal model delta sinusoidal sigma weight residual -30.00 -88.89 58.89 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 7851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1543 0.053 - 0.107: 394 0.107 - 0.160: 61 0.160 - 0.213: 4 0.213 - 0.267: 2 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CG LEU C 585 " pdb=" CB LEU C 585 " pdb=" CD1 LEU C 585 " pdb=" CD2 LEU C 585 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE T 448 " pdb=" N ILE T 448 " pdb=" C ILE T 448 " pdb=" CB ILE T 448 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 2001 not shown) Planarity restraints: 2221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU U 69 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LEU U 69 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU U 69 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL U 70 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 77 " 0.002 2.00e-02 2.50e+03 1.83e-02 5.03e+00 pdb=" CG HIS R 77 " -0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS R 77 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS R 77 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS R 77 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS R 77 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 17 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO D 18 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 18 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 18 " -0.031 5.00e-02 4.00e+02 ... (remaining 2218 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 143 2.58 - 3.16: 11246 3.16 - 3.74: 19617 3.74 - 4.32: 26535 4.32 - 4.90: 43525 Nonbonded interactions: 101066 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.998 2.230 nonbonded pdb=" OD1 ASP C 396 " pdb=" OH TYR C 455 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASP T 201 " pdb=" OG SER T 204 " model vdw 2.212 3.040 nonbonded pdb=" O SER C 550 " pdb=" OG SER C 550 " model vdw 2.241 3.040 nonbonded pdb=" O THR S 101 " pdb=" OG1 THR S 104 " model vdw 2.258 3.040 ... (remaining 101061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.710 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.007 0.274 12987 Z= 0.309 Angle : 0.884 10.205 17555 Z= 0.529 Chirality : 0.047 0.267 2004 Planarity : 0.004 0.056 2220 Dihedral : 15.099 89.634 4779 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.29 % Allowed : 7.85 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1560 helix: -0.55 (0.18), residues: 726 sheet: -1.63 (0.33), residues: 215 loop : -3.52 (0.20), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 368 HIS 0.027 0.002 HIS R 77 PHE 0.013 0.002 PHE C 508 TYR 0.017 0.002 TYR C 377 ARG 0.005 0.000 ARG C 506 Details of bonding type rmsd link_TRANS : bond 0.00681 ( 1) link_TRANS : angle 0.76645 ( 3) hydrogen bonds : bond 0.14351 ( 664) hydrogen bonds : angle 6.39898 ( 1920) metal coordination : bond 0.08661 ( 11) metal coordination : angle 4.53678 ( 6) SS BOND : bond 0.01742 ( 2) SS BOND : angle 2.22696 ( 4) covalent geometry : bond 0.00597 (12972) covalent geometry : angle 0.88014 (17542) Misc. bond : bond 0.11774 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 353 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8100 (mmm) cc_final: 0.7887 (mmp) REVERT: T 230 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7455 (mt-10) REVERT: T 277 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7523 (tm-30) REVERT: T 322 ASP cc_start: 0.7901 (m-30) cc_final: 0.7687 (t70) REVERT: T 440 VAL cc_start: 0.9051 (t) cc_final: 0.8835 (p) REVERT: T 581 ASP cc_start: 0.8785 (t70) cc_final: 0.8222 (p0) REVERT: S 13 ILE cc_start: 0.7421 (tp) cc_final: 0.7065 (tt) REVERT: S 48 ILE cc_start: 0.9131 (mp) cc_final: 0.8241 (mp) REVERT: S 108 MET cc_start: 0.7670 (mtp) cc_final: 0.6957 (mmp) REVERT: S 113 THR cc_start: 0.7942 (p) cc_final: 0.6983 (p) REVERT: S 122 ASN cc_start: 0.8611 (t0) cc_final: 0.8410 (t0) REVERT: C 147 ARG cc_start: 0.5345 (mmt180) cc_final: 0.3502 (mmt180) REVERT: C 188 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7979 (tm-30) REVERT: N 24 GLU cc_start: 0.8531 (tp30) cc_final: 0.8190 (tp30) REVERT: D 16 ASP cc_start: 0.7716 (m-30) cc_final: 0.7440 (t0) REVERT: D 63 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8742 (mmtp) outliers start: 4 outliers final: 1 residues processed: 357 average time/residue: 0.3072 time to fit residues: 148.8640 Evaluate side-chains 235 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 43 ASN S 59 HIS C 214 ASN C 308 GLN C 309 ASN C 602 GLN C 727 HIS N 49 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100218 restraints weight = 26498.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101058 restraints weight = 18944.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101681 restraints weight = 19314.560| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12987 Z= 0.149 Angle : 0.631 8.312 17555 Z= 0.330 Chirality : 0.043 0.221 2004 Planarity : 0.004 0.045 2220 Dihedral : 4.181 69.485 1729 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.11 % Allowed : 16.36 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1560 helix: 0.77 (0.19), residues: 726 sheet: -1.01 (0.35), residues: 213 loop : -2.87 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 248 HIS 0.008 0.001 HIS R 82 PHE 0.014 0.002 PHE C 95 TYR 0.023 0.002 TYR T 438 ARG 0.011 0.001 ARG T 234 Details of bonding type rmsd link_TRANS : bond 0.00266 ( 1) link_TRANS : angle 0.35784 ( 3) hydrogen bonds : bond 0.04931 ( 664) hydrogen bonds : angle 5.07821 ( 1920) metal coordination : bond 0.02604 ( 11) metal coordination : angle 5.50847 ( 6) SS BOND : bond 0.00306 ( 2) SS BOND : angle 2.47742 ( 4) covalent geometry : bond 0.00331 (12972) covalent geometry : angle 0.62150 (17542) Misc. bond : bond 0.00171 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8112 (mmm) cc_final: 0.7840 (mmp) REVERT: T 230 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7448 (mt-10) REVERT: T 277 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7457 (tm-30) REVERT: T 322 ASP cc_start: 0.7878 (m-30) cc_final: 0.7676 (t70) REVERT: T 581 ASP cc_start: 0.8726 (t70) cc_final: 0.8314 (p0) REVERT: S 108 MET cc_start: 0.7576 (mtp) cc_final: 0.6825 (mmm) REVERT: S 122 ASN cc_start: 0.8602 (t0) cc_final: 0.8378 (t0) REVERT: C 147 ARG cc_start: 0.5367 (mmt180) cc_final: 0.3827 (mmt180) REVERT: C 681 ARG cc_start: 0.6887 (mmm-85) cc_final: 0.6344 (tpp80) REVERT: N 24 GLU cc_start: 0.8281 (tp30) cc_final: 0.7969 (tp30) REVERT: R 76 ASN cc_start: 0.8490 (m-40) cc_final: 0.7492 (t0) REVERT: R 88 LEU cc_start: 0.8760 (mm) cc_final: 0.8385 (mm) REVERT: D 16 ASP cc_start: 0.7683 (m-30) cc_final: 0.7434 (t0) REVERT: D 63 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8700 (mmtp) REVERT: D 112 ASP cc_start: 0.8115 (m-30) cc_final: 0.7542 (m-30) REVERT: U 25 ASN cc_start: 0.8657 (m110) cc_final: 0.8377 (m110) outliers start: 29 outliers final: 19 residues processed: 287 average time/residue: 0.2262 time to fit residues: 97.3967 Evaluate side-chains 244 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 82 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 59 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN U 49 GLN I 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099401 restraints weight = 26746.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100156 restraints weight = 18979.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100902 restraints weight = 18344.291| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 12987 Z= 0.147 Angle : 0.598 7.008 17555 Z= 0.311 Chirality : 0.042 0.195 2004 Planarity : 0.003 0.037 2220 Dihedral : 4.373 66.840 1729 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.20 % Allowed : 18.76 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1560 helix: 1.04 (0.19), residues: 724 sheet: -0.78 (0.35), residues: 219 loop : -2.46 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 531 HIS 0.008 0.001 HIS R 82 PHE 0.016 0.001 PHE C 595 TYR 0.015 0.001 TYR T 251 ARG 0.007 0.000 ARG C 34 Details of bonding type rmsd link_TRANS : bond 0.00427 ( 1) link_TRANS : angle 0.70236 ( 3) hydrogen bonds : bond 0.04546 ( 664) hydrogen bonds : angle 4.81509 ( 1920) metal coordination : bond 0.04553 ( 11) metal coordination : angle 4.47706 ( 6) SS BOND : bond 0.00902 ( 2) SS BOND : angle 3.92251 ( 4) covalent geometry : bond 0.00324 (12972) covalent geometry : angle 0.58985 (17542) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8205 (mmm) cc_final: 0.7957 (mmp) REVERT: T 277 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7488 (tm-30) REVERT: T 322 ASP cc_start: 0.7991 (m-30) cc_final: 0.7680 (t70) REVERT: S 14 PHE cc_start: 0.7541 (t80) cc_final: 0.7206 (t80) REVERT: S 122 ASN cc_start: 0.8616 (t0) cc_final: 0.8336 (t0) REVERT: C 147 ARG cc_start: 0.5498 (mmt180) cc_final: 0.3831 (mmt180) REVERT: C 187 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 188 GLU cc_start: 0.8583 (tp30) cc_final: 0.7282 (tp30) REVERT: C 191 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7448 (ptp-110) REVERT: C 613 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7264 (tp40) REVERT: C 681 ARG cc_start: 0.6941 (mmm-85) cc_final: 0.6519 (tpp80) REVERT: C 724 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7608 (m) REVERT: N 24 GLU cc_start: 0.8319 (tp30) cc_final: 0.7932 (tp30) REVERT: R 23 GLU cc_start: 0.5192 (mp0) cc_final: 0.4949 (mp0) REVERT: R 76 ASN cc_start: 0.8573 (m-40) cc_final: 0.7550 (t0) REVERT: R 88 LEU cc_start: 0.8744 (mm) cc_final: 0.8415 (mm) REVERT: D 16 ASP cc_start: 0.7728 (m-30) cc_final: 0.7439 (t0) REVERT: D 63 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8604 (mmtp) REVERT: D 112 ASP cc_start: 0.7927 (m-30) cc_final: 0.7669 (m-30) REVERT: U 25 ASN cc_start: 0.8713 (m110) cc_final: 0.8394 (m110) outliers start: 44 outliers final: 26 residues processed: 270 average time/residue: 0.2630 time to fit residues: 104.5329 Evaluate side-chains 248 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100162 restraints weight = 26311.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100704 restraints weight = 18667.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101605 restraints weight = 17876.713| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 12987 Z= 0.127 Angle : 0.592 11.078 17555 Z= 0.301 Chirality : 0.041 0.185 2004 Planarity : 0.003 0.060 2220 Dihedral : 4.372 65.824 1729 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.05 % Allowed : 19.35 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1560 helix: 1.15 (0.19), residues: 724 sheet: -0.67 (0.35), residues: 224 loop : -2.32 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 70 HIS 0.019 0.001 HIS S 59 PHE 0.010 0.001 PHE C 566 TYR 0.012 0.001 TYR C 278 ARG 0.006 0.000 ARG T 187 Details of bonding type rmsd link_TRANS : bond 0.00524 ( 1) link_TRANS : angle 0.83931 ( 3) hydrogen bonds : bond 0.04228 ( 664) hydrogen bonds : angle 4.73486 ( 1920) metal coordination : bond 0.04016 ( 11) metal coordination : angle 6.04264 ( 6) SS BOND : bond 0.00208 ( 2) SS BOND : angle 5.75648 ( 4) covalent geometry : bond 0.00277 (12972) covalent geometry : angle 0.57535 (17542) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8277 (mmm) cc_final: 0.8013 (mmp) REVERT: T 230 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7350 (mp0) REVERT: T 277 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7538 (tm-30) REVERT: T 322 ASP cc_start: 0.7964 (m-30) cc_final: 0.7666 (t70) REVERT: T 478 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7787 (mm) REVERT: S 122 ASN cc_start: 0.8550 (t0) cc_final: 0.8202 (t0) REVERT: C 147 ARG cc_start: 0.5668 (mmt180) cc_final: 0.3900 (mmt180) REVERT: C 151 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4838 (pm20) REVERT: C 187 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8325 (mt) REVERT: C 188 GLU cc_start: 0.8632 (tp30) cc_final: 0.7980 (tp30) REVERT: C 276 GLN cc_start: 0.8481 (tt0) cc_final: 0.8160 (tm-30) REVERT: C 540 LEU cc_start: 0.8984 (mt) cc_final: 0.8641 (mp) REVERT: C 602 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: C 613 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7170 (tp40) REVERT: C 681 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6848 (tpp80) REVERT: C 724 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7506 (m) REVERT: N 11 LYS cc_start: 0.8678 (tttp) cc_final: 0.8344 (ptmt) REVERT: R 23 GLU cc_start: 0.5518 (mp0) cc_final: 0.5316 (mp0) REVERT: R 56 CYS cc_start: 0.0919 (OUTLIER) cc_final: 0.0670 (t) REVERT: R 76 ASN cc_start: 0.8556 (m-40) cc_final: 0.7505 (t0) REVERT: R 88 LEU cc_start: 0.8711 (mm) cc_final: 0.8409 (mm) REVERT: D 63 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8587 (mmtp) REVERT: D 112 ASP cc_start: 0.8015 (m-30) cc_final: 0.7571 (m-30) REVERT: U 15 LEU cc_start: 0.8589 (mm) cc_final: 0.8349 (mp) REVERT: U 25 ASN cc_start: 0.8710 (m110) cc_final: 0.8367 (m110) outliers start: 42 outliers final: 27 residues processed: 266 average time/residue: 0.2645 time to fit residues: 104.1986 Evaluate side-chains 258 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 472 LEU Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 602 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 126 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS C 206 GLN C 284 GLN ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098533 restraints weight = 26658.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099440 restraints weight = 18737.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100056 restraints weight = 16806.265| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 12987 Z= 0.152 Angle : 0.588 9.380 17555 Z= 0.302 Chirality : 0.041 0.181 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.362 61.661 1728 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.56 % Allowed : 20.65 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1560 helix: 1.21 (0.19), residues: 725 sheet: -0.53 (0.36), residues: 212 loop : -2.17 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 70 HIS 0.010 0.001 HIS R 82 PHE 0.014 0.001 PHE C 606 TYR 0.014 0.001 TYR C 278 ARG 0.002 0.000 ARG C 34 Details of bonding type rmsd link_TRANS : bond 0.00348 ( 1) link_TRANS : angle 0.17138 ( 3) hydrogen bonds : bond 0.04316 ( 664) hydrogen bonds : angle 4.68057 ( 1920) metal coordination : bond 0.04286 ( 11) metal coordination : angle 5.53259 ( 6) SS BOND : bond 0.00330 ( 2) SS BOND : angle 4.02907 ( 4) covalent geometry : bond 0.00340 (12972) covalent geometry : angle 0.57653 (17542) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8251 (mmm) cc_final: 0.7979 (mmp) REVERT: T 230 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7445 (mp0) REVERT: T 245 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8160 (ttm170) REVERT: T 277 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7534 (tm-30) REVERT: T 322 ASP cc_start: 0.7886 (m-30) cc_final: 0.7607 (t70) REVERT: S 122 ASN cc_start: 0.8507 (t0) cc_final: 0.8128 (t0) REVERT: C 147 ARG cc_start: 0.6088 (mmt180) cc_final: 0.4078 (mmt180) REVERT: C 188 GLU cc_start: 0.8684 (tp30) cc_final: 0.7991 (tp30) REVERT: C 540 LEU cc_start: 0.9000 (mt) cc_final: 0.8790 (mp) REVERT: C 602 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: C 681 ARG cc_start: 0.7182 (mmm-85) cc_final: 0.6795 (tpp80) REVERT: C 724 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7489 (m) REVERT: N 24 GLU cc_start: 0.8373 (tp30) cc_final: 0.8018 (tp30) REVERT: R 23 GLU cc_start: 0.5817 (mp0) cc_final: 0.5561 (mp0) REVERT: R 76 ASN cc_start: 0.8651 (m-40) cc_final: 0.7510 (t0) REVERT: R 88 LEU cc_start: 0.8714 (mm) cc_final: 0.8455 (mm) REVERT: D 16 ASP cc_start: 0.7628 (m-30) cc_final: 0.7325 (t0) REVERT: D 63 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8614 (mmtp) REVERT: U 25 ASN cc_start: 0.8706 (m110) cc_final: 0.8365 (m110) REVERT: U 41 GLN cc_start: 0.7509 (mt0) cc_final: 0.7268 (mt0) outliers start: 49 outliers final: 31 residues processed: 256 average time/residue: 0.3312 time to fit residues: 127.2301 Evaluate side-chains 254 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 245 ARG Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 472 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 602 GLN Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 388 HIS C 615 ASN C 683 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099326 restraints weight = 27189.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100240 restraints weight = 19077.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100849 restraints weight = 17028.672| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 12987 Z= 0.128 Angle : 0.583 9.541 17555 Z= 0.297 Chirality : 0.041 0.174 2004 Planarity : 0.003 0.050 2220 Dihedral : 4.371 60.811 1728 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.98 % Allowed : 22.11 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1560 helix: 1.30 (0.19), residues: 725 sheet: -0.35 (0.37), residues: 204 loop : -2.19 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 55 HIS 0.010 0.001 HIS R 82 PHE 0.017 0.001 PHE T 566 TYR 0.013 0.001 TYR C 278 ARG 0.005 0.000 ARG U 42 Details of bonding type rmsd link_TRANS : bond 0.00547 ( 1) link_TRANS : angle 0.40600 ( 3) hydrogen bonds : bond 0.04080 ( 664) hydrogen bonds : angle 4.63075 ( 1920) metal coordination : bond 0.04304 ( 11) metal coordination : angle 5.52653 ( 6) SS BOND : bond 0.00268 ( 2) SS BOND : angle 5.35035 ( 4) covalent geometry : bond 0.00283 (12972) covalent geometry : angle 0.56827 (17542) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8243 (mmm) cc_final: 0.7978 (mmp) REVERT: T 230 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7437 (mp0) REVERT: T 245 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8179 (ttm110) REVERT: T 277 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7520 (tm-30) REVERT: T 322 ASP cc_start: 0.7867 (m-30) cc_final: 0.7587 (t70) REVERT: S 122 ASN cc_start: 0.8430 (t0) cc_final: 0.8049 (t0) REVERT: C 147 ARG cc_start: 0.6020 (mmt90) cc_final: 0.4038 (mmt180) REVERT: C 188 GLU cc_start: 0.8677 (tp30) cc_final: 0.7988 (tp30) REVERT: C 276 GLN cc_start: 0.8489 (tt0) cc_final: 0.8112 (tm-30) REVERT: C 577 ARG cc_start: 0.6929 (ptt180) cc_final: 0.6436 (ptp-170) REVERT: C 602 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: C 613 GLN cc_start: 0.8201 (tp40) cc_final: 0.7602 (tt0) REVERT: C 681 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6560 (tpp80) REVERT: C 724 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7509 (m) REVERT: R 76 ASN cc_start: 0.8631 (m-40) cc_final: 0.7489 (t0) REVERT: R 88 LEU cc_start: 0.8663 (mm) cc_final: 0.8427 (mm) REVERT: D 16 ASP cc_start: 0.7660 (m-30) cc_final: 0.7255 (t0) REVERT: D 63 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8600 (mmtp) REVERT: U 15 LEU cc_start: 0.8602 (mm) cc_final: 0.8336 (mp) REVERT: U 25 ASN cc_start: 0.8685 (m110) cc_final: 0.8338 (m110) outliers start: 41 outliers final: 30 residues processed: 256 average time/residue: 0.2462 time to fit residues: 92.8429 Evaluate side-chains 255 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 245 ARG Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 472 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 602 GLN Chi-restraints excluded: chain C residue 614 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 136 optimal weight: 0.0060 chunk 131 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS C 214 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100180 restraints weight = 26762.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100917 restraints weight = 19082.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101767 restraints weight = 17765.606| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 12987 Z= 0.123 Angle : 0.580 9.010 17555 Z= 0.295 Chirality : 0.041 0.171 2004 Planarity : 0.003 0.083 2220 Dihedral : 4.313 59.295 1728 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.27 % Allowed : 23.05 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1560 helix: 1.34 (0.19), residues: 728 sheet: -0.31 (0.36), residues: 211 loop : -2.15 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 55 HIS 0.009 0.001 HIS R 82 PHE 0.018 0.001 PHE T 566 TYR 0.013 0.001 TYR C 278 ARG 0.005 0.000 ARG T 187 Details of bonding type rmsd link_TRANS : bond 0.00411 ( 1) link_TRANS : angle 0.28500 ( 3) hydrogen bonds : bond 0.03960 ( 664) hydrogen bonds : angle 4.57197 ( 1920) metal coordination : bond 0.04258 ( 11) metal coordination : angle 5.29451 ( 6) SS BOND : bond 0.00810 ( 2) SS BOND : angle 4.03416 ( 4) covalent geometry : bond 0.00267 (12972) covalent geometry : angle 0.56835 (17542) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8252 (mmm) cc_final: 0.7961 (mmp) REVERT: T 230 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7406 (mp0) REVERT: T 277 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7512 (tm-30) REVERT: T 322 ASP cc_start: 0.7814 (m-30) cc_final: 0.7545 (t70) REVERT: S 55 TRP cc_start: 0.8329 (t60) cc_final: 0.7838 (t60) REVERT: S 119 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8113 (mmtt) REVERT: S 122 ASN cc_start: 0.8435 (t0) cc_final: 0.8068 (t0) REVERT: C 147 ARG cc_start: 0.6232 (mmt90) cc_final: 0.4107 (mmt180) REVERT: C 188 GLU cc_start: 0.8697 (tp30) cc_final: 0.7947 (tp30) REVERT: C 276 GLN cc_start: 0.8457 (tt0) cc_final: 0.8054 (tm-30) REVERT: C 577 ARG cc_start: 0.6847 (ptt180) cc_final: 0.6373 (ptp-170) REVERT: C 608 MET cc_start: 0.6096 (mtm) cc_final: 0.5830 (mtt) REVERT: C 681 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6529 (tpp80) REVERT: C 724 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7605 (m) REVERT: R 55 GLU cc_start: 0.6629 (tp30) cc_final: 0.6289 (tp30) REVERT: R 76 ASN cc_start: 0.8706 (m-40) cc_final: 0.7523 (t0) REVERT: R 88 LEU cc_start: 0.8661 (mm) cc_final: 0.8449 (mm) REVERT: D 12 ASP cc_start: 0.8358 (m-30) cc_final: 0.8095 (t0) REVERT: D 16 ASP cc_start: 0.7562 (m-30) cc_final: 0.7338 (t0) REVERT: D 60 TYR cc_start: 0.8726 (t80) cc_final: 0.8483 (t80) REVERT: D 63 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8593 (mmtp) REVERT: U 15 LEU cc_start: 0.8615 (mm) cc_final: 0.8351 (mp) REVERT: U 25 ASN cc_start: 0.8670 (m110) cc_final: 0.8321 (m110) outliers start: 45 outliers final: 31 residues processed: 256 average time/residue: 0.2785 time to fit residues: 104.7906 Evaluate side-chains 248 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 136 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 388 HIS S 54 GLN C 214 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.126568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099426 restraints weight = 27083.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099846 restraints weight = 19210.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100404 restraints weight = 18440.850| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 12987 Z= 0.138 Angle : 0.600 8.838 17555 Z= 0.305 Chirality : 0.042 0.169 2004 Planarity : 0.003 0.046 2220 Dihedral : 4.286 56.321 1728 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.76 % Allowed : 23.56 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1560 helix: 1.39 (0.19), residues: 728 sheet: -0.20 (0.36), residues: 209 loop : -2.15 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 531 HIS 0.013 0.001 HIS T 191 PHE 0.022 0.001 PHE S 14 TYR 0.014 0.001 TYR C 278 ARG 0.004 0.000 ARG T 245 Details of bonding type rmsd link_TRANS : bond 0.00307 ( 1) link_TRANS : angle 0.46971 ( 3) hydrogen bonds : bond 0.04015 ( 664) hydrogen bonds : angle 4.59295 ( 1920) metal coordination : bond 0.04151 ( 11) metal coordination : angle 5.40518 ( 6) SS BOND : bond 0.00500 ( 2) SS BOND : angle 3.70109 ( 4) covalent geometry : bond 0.00309 (12972) covalent geometry : angle 0.58876 (17542) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8244 (mmm) cc_final: 0.8008 (mmp) REVERT: T 230 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7415 (mp0) REVERT: T 277 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7489 (tm-30) REVERT: T 322 ASP cc_start: 0.7778 (m-30) cc_final: 0.7538 (t70) REVERT: S 119 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8178 (mmtt) REVERT: S 122 ASN cc_start: 0.8421 (t0) cc_final: 0.8057 (t0) REVERT: C 147 ARG cc_start: 0.6294 (mmt90) cc_final: 0.4192 (mmt180) REVERT: C 188 GLU cc_start: 0.8710 (tp30) cc_final: 0.7386 (tp30) REVERT: C 191 ARG cc_start: 0.8047 (ptp-110) cc_final: 0.7425 (ptp-110) REVERT: C 276 GLN cc_start: 0.8452 (tt0) cc_final: 0.8055 (tm-30) REVERT: C 577 ARG cc_start: 0.6831 (ptt180) cc_final: 0.6319 (ptp-170) REVERT: C 681 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6643 (tpp80) REVERT: C 724 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7581 (m) REVERT: R 52 LEU cc_start: 0.7938 (pt) cc_final: 0.7610 (tt) REVERT: R 76 ASN cc_start: 0.8758 (m-40) cc_final: 0.7547 (t0) REVERT: D 16 ASP cc_start: 0.7634 (m-30) cc_final: 0.7336 (t0) REVERT: D 60 TYR cc_start: 0.8728 (t80) cc_final: 0.8521 (t80) REVERT: D 63 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8615 (mmtp) REVERT: U 15 LEU cc_start: 0.8619 (mm) cc_final: 0.8372 (mp) REVERT: U 25 ASN cc_start: 0.8702 (m110) cc_final: 0.8349 (m110) REVERT: U 49 GLN cc_start: 0.8654 (mm110) cc_final: 0.8260 (tp40) outliers start: 38 outliers final: 31 residues processed: 243 average time/residue: 0.3105 time to fit residues: 113.3430 Evaluate side-chains 242 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 338 ILE Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 614 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 388 HIS C 214 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099491 restraints weight = 26939.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100577 restraints weight = 18451.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101170 restraints weight = 18092.305| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 12987 Z= 0.133 Angle : 0.595 8.198 17555 Z= 0.304 Chirality : 0.042 0.183 2004 Planarity : 0.003 0.040 2220 Dihedral : 4.243 53.003 1728 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.76 % Allowed : 24.00 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1560 helix: 1.46 (0.19), residues: 728 sheet: -0.17 (0.36), residues: 208 loop : -2.06 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 PHE 0.012 0.001 PHE C 606 TYR 0.014 0.001 TYR C 278 ARG 0.005 0.000 ARG D 136 Details of bonding type rmsd link_TRANS : bond 0.00329 ( 1) link_TRANS : angle 0.33969 ( 3) hydrogen bonds : bond 0.03954 ( 664) hydrogen bonds : angle 4.55906 ( 1920) metal coordination : bond 0.04130 ( 11) metal coordination : angle 5.10559 ( 6) SS BOND : bond 0.00534 ( 2) SS BOND : angle 3.46480 ( 4) covalent geometry : bond 0.00296 (12972) covalent geometry : angle 0.58552 (17542) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8204 (mmm) cc_final: 0.7979 (mmp) REVERT: T 230 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7442 (mp0) REVERT: T 277 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7550 (tm-30) REVERT: T 322 ASP cc_start: 0.7815 (m-30) cc_final: 0.7537 (t70) REVERT: S 55 TRP cc_start: 0.8386 (t60) cc_final: 0.7941 (t60) REVERT: S 119 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8188 (mmtt) REVERT: S 122 ASN cc_start: 0.8426 (t0) cc_final: 0.8068 (t0) REVERT: C 147 ARG cc_start: 0.6498 (mmt90) cc_final: 0.4407 (mmt180) REVERT: C 276 GLN cc_start: 0.8483 (tt0) cc_final: 0.8082 (tm-30) REVERT: C 555 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6719 (tt) REVERT: C 577 ARG cc_start: 0.6803 (ptt180) cc_final: 0.6299 (ptp-170) REVERT: C 633 MET cc_start: 0.7585 (ppp) cc_final: 0.6178 (mmp) REVERT: C 681 ARG cc_start: 0.6977 (mmm-85) cc_final: 0.6572 (tpp80) REVERT: N 11 LYS cc_start: 0.8630 (tttp) cc_final: 0.8419 (ptmt) REVERT: R 76 ASN cc_start: 0.8799 (m-40) cc_final: 0.7603 (t0) REVERT: D 63 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8570 (mmtp) REVERT: U 15 LEU cc_start: 0.8601 (mm) cc_final: 0.8355 (mp) REVERT: U 25 ASN cc_start: 0.8691 (m110) cc_final: 0.8328 (m110) REVERT: U 49 GLN cc_start: 0.8628 (mm110) cc_final: 0.8333 (tp40) outliers start: 38 outliers final: 34 residues processed: 242 average time/residue: 0.3197 time to fit residues: 116.3849 Evaluate side-chains 249 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain U residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 154 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.128033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100867 restraints weight = 26795.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101946 restraints weight = 18484.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102642 restraints weight = 17616.007| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 12987 Z= 0.119 Angle : 0.620 12.684 17555 Z= 0.308 Chirality : 0.041 0.224 2004 Planarity : 0.003 0.039 2220 Dihedral : 4.188 52.394 1728 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.55 % Allowed : 24.44 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1560 helix: 1.53 (0.19), residues: 728 sheet: -0.02 (0.37), residues: 207 loop : -2.03 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 PHE 0.022 0.001 PHE S 14 TYR 0.013 0.001 TYR D 60 ARG 0.003 0.000 ARG R 46 Details of bonding type rmsd link_TRANS : bond 0.00296 ( 1) link_TRANS : angle 0.35305 ( 3) hydrogen bonds : bond 0.03850 ( 664) hydrogen bonds : angle 4.49842 ( 1920) metal coordination : bond 0.03920 ( 11) metal coordination : angle 5.28743 ( 6) SS BOND : bond 0.00441 ( 2) SS BOND : angle 2.86097 ( 4) covalent geometry : bond 0.00258 (12972) covalent geometry : angle 0.61063 (17542) Misc. bond : bond 0.00034 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8185 (mmm) cc_final: 0.7977 (mmp) REVERT: T 277 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7593 (tm-30) REVERT: T 322 ASP cc_start: 0.7817 (m-30) cc_final: 0.7528 (t70) REVERT: S 55 TRP cc_start: 0.8356 (t60) cc_final: 0.7889 (t60) REVERT: S 119 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8182 (mmtt) REVERT: S 122 ASN cc_start: 0.8364 (t0) cc_final: 0.8003 (t0) REVERT: C 32 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.5698 (t80) REVERT: C 147 ARG cc_start: 0.6419 (mmt90) cc_final: 0.4279 (mmt90) REVERT: C 188 GLU cc_start: 0.8691 (tp30) cc_final: 0.7831 (tp30) REVERT: C 191 ARG cc_start: 0.8054 (ptp-110) cc_final: 0.7726 (ptp-110) REVERT: C 276 GLN cc_start: 0.8449 (tt0) cc_final: 0.8065 (tm-30) REVERT: C 555 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6496 (tt) REVERT: C 633 MET cc_start: 0.7528 (ppp) cc_final: 0.6176 (mmp) REVERT: C 681 ARG cc_start: 0.6961 (mmm-85) cc_final: 0.6577 (tpp80) REVERT: R 51 ASP cc_start: 0.7459 (t0) cc_final: 0.7241 (t0) REVERT: R 52 LEU cc_start: 0.7982 (pt) cc_final: 0.7669 (tt) REVERT: R 76 ASN cc_start: 0.8754 (m-40) cc_final: 0.7547 (t0) REVERT: D 16 ASP cc_start: 0.7832 (m-30) cc_final: 0.7450 (t0) REVERT: D 63 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8565 (mmtp) REVERT: D 66 LYS cc_start: 0.8635 (mttt) cc_final: 0.8230 (ttpt) REVERT: U 25 ASN cc_start: 0.8641 (m110) cc_final: 0.8289 (m110) REVERT: U 41 GLN cc_start: 0.6683 (pm20) cc_final: 0.6063 (pm20) outliers start: 35 outliers final: 32 residues processed: 250 average time/residue: 0.3212 time to fit residues: 120.1010 Evaluate side-chains 250 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain U residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS C 574 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098165 restraints weight = 26837.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099467 restraints weight = 18858.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099956 restraints weight = 16954.017| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 12987 Z= 0.174 Angle : 0.646 12.161 17555 Z= 0.329 Chirality : 0.043 0.176 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.265 49.337 1728 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.91 % Allowed : 24.44 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1560 helix: 1.46 (0.19), residues: 726 sheet: -0.26 (0.36), residues: 209 loop : -2.02 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP S 55 HIS 0.008 0.001 HIS T 191 PHE 0.022 0.001 PHE T 566 TYR 0.022 0.001 TYR C 278 ARG 0.007 0.000 ARG C 506 Details of bonding type rmsd link_TRANS : bond 0.00203 ( 1) link_TRANS : angle 0.16480 ( 3) hydrogen bonds : bond 0.04227 ( 664) hydrogen bonds : angle 4.61601 ( 1920) metal coordination : bond 0.04112 ( 11) metal coordination : angle 5.02885 ( 6) SS BOND : bond 0.00448 ( 2) SS BOND : angle 3.29373 ( 4) covalent geometry : bond 0.00399 (12972) covalent geometry : angle 0.63794 (17542) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4896.31 seconds wall clock time: 90 minutes 26.66 seconds (5426.66 seconds total)