Starting phenix.real_space_refine on Thu Sep 18 00:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ttu_10585/09_2025/6ttu_10585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ttu_10585/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ttu_10585/09_2025/6ttu_10585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ttu_10585/09_2025/6ttu_10585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ttu_10585/09_2025/6ttu_10585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ttu_10585/09_2025/6ttu_10585.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} 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: {'GLU:plan': 7, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN: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: {'ASN:plan1': 1, 'GLU:plan': 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: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU: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: 2.63, per 1000 atoms: 0.21 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: 1.21 Conformation dependent library (CDL) restraints added in 478.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 2.08 Time building geometry restraints manager: 1.52 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: 2.800 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- 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 : 13.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG C 506 TYR 0.017 0.002 TYR C 377 PHE 0.013 0.002 PHE C 508 TRP 0.018 0.002 TRP T 368 HIS 0.027 0.002 HIS R 77 Details of bonding type rmsd covalent geometry : bond 0.00597 (12972) covalent geometry : angle 0.88014 (17542) SS BOND : bond 0.01742 ( 2) SS BOND : angle 2.22696 ( 4) hydrogen bonds : bond 0.14351 ( 664) hydrogen bonds : angle 6.39898 ( 1920) metal coordination : bond 0.08661 ( 11) metal coordination : angle 4.53678 ( 6) Misc. bond : bond 0.11774 ( 1) link_TRANS : bond 0.00681 ( 1) link_TRANS : angle 0.76645 ( 3) *********************** 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 : 0.549 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: 0.7451 (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: 0.8838 (p) REVERT: T 581 ASP cc_start: 0.8785 (t70) cc_final: 0.8223 (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: 0.8243 (mp) REVERT: S 108 MET cc_start: 0.7670 (mtp) cc_final: 0.6958 (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: 0.1371 time to fit residues: 66.5737 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 : 0.524 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.126200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099072 restraints weight = 26570.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100655 restraints weight = 18441.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101108 restraints weight = 18063.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101637 restraints weight = 12057.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102189 restraints weight = 10834.097| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 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 = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12987 Z= 0.168 Angle : 0.641 8.054 17555 Z= 0.336 Chirality : 0.044 0.221 2004 Planarity : 0.004 0.046 2220 Dihedral : 4.280 69.206 1729 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.18 % Allowed : 16.36 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.21), residues: 1560 helix: 0.75 (0.19), residues: 720 sheet: -0.96 (0.35), residues: 217 loop : -2.84 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 234 TYR 0.025 0.002 TYR T 438 PHE 0.015 0.002 PHE C 95 TRP 0.025 0.002 TRP T 248 HIS 0.010 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00375 (12972) covalent geometry : angle 0.63170 (17542) SS BOND : bond 0.00338 ( 2) SS BOND : angle 2.61182 ( 4) hydrogen bonds : bond 0.05020 ( 664) hydrogen bonds : angle 5.11634 ( 1920) metal coordination : bond 0.01723 ( 11) metal coordination : angle 5.56320 ( 6) Misc. bond : bond 0.00109 ( 1) link_TRANS : bond 0.00247 ( 1) link_TRANS : angle 0.47070 ( 3) *********************** 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 295 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8145 (mmm) cc_final: 0.7847 (mmp) REVERT: T 230 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7462 (mt-10) REVERT: T 277 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7437 (tm-30) REVERT: T 322 ASP cc_start: 0.7909 (m-30) cc_final: 0.7625 (t70) REVERT: T 360 SER cc_start: 0.9213 (t) cc_final: 0.9000 (p) REVERT: T 581 ASP cc_start: 0.8781 (t70) cc_final: 0.8262 (p0) REVERT: S 116 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7996 (tt0) REVERT: S 122 ASN cc_start: 0.8630 (t0) cc_final: 0.8424 (t0) REVERT: C 147 ARG cc_start: 0.5446 (mmt180) cc_final: 0.4027 (mmt180) REVERT: C 188 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8163 (tp30) REVERT: C 681 ARG cc_start: 0.6876 (mmm-85) cc_final: 0.6515 (tpp80) REVERT: C 716 VAL cc_start: 0.8895 (p) cc_final: 0.8636 (p) REVERT: C 719 MET cc_start: 0.8336 (mmm) cc_final: 0.8057 (mtm) REVERT: R 23 GLU cc_start: 0.5565 (mp0) cc_final: 0.5358 (mp0) REVERT: R 76 ASN cc_start: 0.8543 (m-40) cc_final: 0.7541 (t0) REVERT: R 88 LEU cc_start: 0.8766 (mm) cc_final: 0.8385 (mm) REVERT: D 16 ASP cc_start: 0.7724 (m-30) cc_final: 0.7424 (t0) REVERT: D 63 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8716 (mmtp) REVERT: D 112 ASP cc_start: 0.8177 (m-30) cc_final: 0.7594 (m-30) REVERT: U 25 ASN cc_start: 0.8700 (m110) cc_final: 0.8396 (m110) outliers start: 30 outliers final: 21 residues processed: 284 average time/residue: 0.0961 time to fit residues: 41.2331 Evaluate side-chains 243 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 N residue 70 VAL Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 109 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.125583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098268 restraints weight = 26911.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100509 restraints weight = 19069.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100796 restraints weight = 16919.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101098 restraints weight = 11434.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101813 restraints weight = 10416.525| |-----------------------------------------------------------------------------| 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 = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 12987 Z= 0.163 Angle : 0.604 6.869 17555 Z= 0.316 Chirality : 0.043 0.189 2004 Planarity : 0.004 0.043 2220 Dihedral : 4.460 65.764 1729 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.20 % Allowed : 19.42 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.21), residues: 1560 helix: 1.04 (0.19), residues: 724 sheet: -0.83 (0.35), residues: 219 loop : -2.51 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.011 0.001 TYR C 377 PHE 0.015 0.001 PHE C 595 TRP 0.018 0.002 TRP T 531 HIS 0.008 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00363 (12972) covalent geometry : angle 0.59598 (17542) SS BOND : bond 0.01247 ( 2) SS BOND : angle 3.47178 ( 4) hydrogen bonds : bond 0.04678 ( 664) hydrogen bonds : angle 4.86158 ( 1920) metal coordination : bond 0.04622 ( 11) metal coordination : angle 4.37556 ( 6) Misc. bond : bond 0.00004 ( 1) link_TRANS : bond 0.00708 ( 1) link_TRANS : angle 0.37974 ( 3) *********************** 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 280 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8170 (mmm) cc_final: 0.7921 (mmp) REVERT: T 277 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7480 (tm-30) REVERT: T 322 ASP cc_start: 0.7978 (m-30) cc_final: 0.7657 (t70) REVERT: T 581 ASP cc_start: 0.8802 (t70) cc_final: 0.8280 (p0) REVERT: S 14 PHE cc_start: 0.7569 (t80) cc_final: 0.7275 (t80) REVERT: S 108 MET cc_start: 0.7570 (mtp) cc_final: 0.6744 (mmp) REVERT: S 122 ASN cc_start: 0.8585 (t0) cc_final: 0.8316 (t0) REVERT: C 147 ARG cc_start: 0.5732 (mmt180) cc_final: 0.4036 (mmt180) REVERT: C 187 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8385 (mt) REVERT: C 188 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8004 (tp30) REVERT: C 613 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7250 (tp40) REVERT: C 681 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6584 (tpp80) REVERT: C 719 MET cc_start: 0.8276 (mmm) cc_final: 0.7971 (mtp) REVERT: C 724 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7640 (m) REVERT: R 76 ASN cc_start: 0.8625 (m-40) cc_final: 0.7620 (t0) REVERT: D 63 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8657 (mmtp) REVERT: U 25 ASN cc_start: 0.8692 (m110) cc_final: 0.8372 (m110) outliers start: 44 outliers final: 27 residues processed: 260 average time/residue: 0.0972 time to fit residues: 38.3757 Evaluate side-chains 243 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 T residue 528 ILE Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain S residue 87 LEU 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 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 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 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 134 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 152 optimal weight: 0.0020 chunk 25 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 overall best weight: 0.7568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098625 restraints weight = 26843.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099385 restraints weight = 18846.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100066 restraints weight = 18021.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101363 restraints weight = 12289.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101563 restraints weight = 10693.700| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 0.7989 moved from start: 0.2853 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= 0.144 Angle : 0.603 10.650 17555 Z= 0.308 Chirality : 0.042 0.205 2004 Planarity : 0.003 0.043 2220 Dihedral : 4.439 64.384 1729 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.20 % Allowed : 20.07 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.21), residues: 1560 helix: 1.15 (0.19), residues: 725 sheet: -0.71 (0.35), residues: 221 loop : -2.37 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 118 TYR 0.013 0.001 TYR C 278 PHE 0.010 0.001 PHE C 95 TRP 0.017 0.002 TRP S 70 HIS 0.024 0.002 HIS S 59 Details of bonding type rmsd covalent geometry : bond 0.00319 (12972) covalent geometry : angle 0.58699 (17542) SS BOND : bond 0.00471 ( 2) SS BOND : angle 5.55800 ( 4) hydrogen bonds : bond 0.04389 ( 664) hydrogen bonds : angle 4.76787 ( 1920) metal coordination : bond 0.04115 ( 11) metal coordination : angle 5.91080 ( 6) Misc. bond : bond 0.00052 ( 1) link_TRANS : bond 0.00562 ( 1) link_TRANS : angle 0.74212 ( 3) *********************** 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 281 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8257 (mmm) cc_final: 0.7984 (mmp) REVERT: T 230 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7345 (mp0) REVERT: T 277 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7519 (tm-30) REVERT: T 322 ASP cc_start: 0.7908 (m-30) cc_final: 0.7585 (t70) REVERT: S 39 VAL cc_start: 0.7168 (t) cc_final: 0.6966 (t) REVERT: S 108 MET cc_start: 0.7578 (mtp) cc_final: 0.6759 (mmp) REVERT: S 122 ASN cc_start: 0.8522 (t0) cc_final: 0.8169 (t0) REVERT: C 147 ARG cc_start: 0.5749 (mmt180) cc_final: 0.3971 (mmt180) REVERT: C 187 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8317 (mt) REVERT: C 276 GLN cc_start: 0.8485 (tt0) cc_final: 0.8148 (tm-30) REVERT: C 540 LEU cc_start: 0.9016 (mt) cc_final: 0.8712 (mp) REVERT: C 602 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: C 613 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7157 (tp40) REVERT: C 681 ARG cc_start: 0.7174 (mmm-85) cc_final: 0.6732 (tpp80) REVERT: C 719 MET cc_start: 0.8281 (mmm) cc_final: 0.8058 (mtp) REVERT: C 724 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7599 (m) REVERT: N 24 GLU cc_start: 0.8300 (tp30) cc_final: 0.7925 (tp30) REVERT: R 21 ARG cc_start: 0.5881 (tpp80) cc_final: 0.5627 (tpp80) REVERT: R 23 GLU cc_start: 0.6225 (mp0) cc_final: 0.5819 (mp0) REVERT: R 56 CYS cc_start: 0.1113 (OUTLIER) cc_final: 0.0897 (t) REVERT: R 76 ASN cc_start: 0.8655 (m-40) cc_final: 0.7560 (t0) REVERT: R 88 LEU cc_start: 0.8717 (mm) cc_final: 0.8416 (mm) REVERT: D 8 LYS cc_start: 0.8519 (tttp) cc_final: 0.8309 (tmtt) REVERT: D 16 ASP cc_start: 0.7623 (m-30) cc_final: 0.7312 (t0) REVERT: D 63 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8602 (mmtp) REVERT: D 112 ASP cc_start: 0.8018 (m-30) cc_final: 0.7573 (m-30) REVERT: U 25 ASN cc_start: 0.8721 (m110) cc_final: 0.8379 (m110) outliers start: 44 outliers final: 28 residues processed: 260 average time/residue: 0.1069 time to fit residues: 41.0528 Evaluate side-chains 249 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 119 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 54 GLN C 206 GLN ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.126828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099525 restraints weight = 26900.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100414 restraints weight = 18637.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100959 restraints weight = 17463.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103055 restraints weight = 12330.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103051 restraints weight = 9461.557| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 12987 Z= 0.126 Angle : 0.572 9.017 17555 Z= 0.293 Chirality : 0.041 0.208 2004 Planarity : 0.003 0.045 2220 Dihedral : 4.349 62.566 1728 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.27 % Allowed : 21.89 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1560 helix: 1.30 (0.19), residues: 724 sheet: -0.51 (0.36), residues: 212 loop : -2.19 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 118 TYR 0.012 0.001 TYR C 278 PHE 0.014 0.001 PHE C 606 TRP 0.014 0.002 TRP S 70 HIS 0.010 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00273 (12972) covalent geometry : angle 0.56093 (17542) SS BOND : bond 0.00196 ( 2) SS BOND : angle 3.93426 ( 4) hydrogen bonds : bond 0.04132 ( 664) hydrogen bonds : angle 4.62957 ( 1920) metal coordination : bond 0.04260 ( 11) metal coordination : angle 5.28649 ( 6) Misc. bond : bond 0.00050 ( 1) link_TRANS : bond 0.00283 ( 1) link_TRANS : angle 0.22004 ( 3) *********************** 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 286 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8260 (mmm) cc_final: 0.7996 (mmp) REVERT: T 230 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7408 (mp0) REVERT: T 245 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8164 (ttm170) REVERT: T 277 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7517 (tm-30) REVERT: T 322 ASP cc_start: 0.7886 (m-30) cc_final: 0.7569 (t70) REVERT: S 54 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: S 108 MET cc_start: 0.7646 (mtp) cc_final: 0.6759 (mmm) REVERT: S 122 ASN cc_start: 0.8448 (t0) cc_final: 0.8043 (t0) REVERT: C 32 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.5866 (t80) REVERT: C 147 ARG cc_start: 0.6158 (mmt180) cc_final: 0.4081 (mmt180) REVERT: C 188 GLU cc_start: 0.8694 (tp30) cc_final: 0.7874 (tp30) REVERT: C 191 ARG cc_start: 0.8196 (ptp-110) cc_final: 0.7901 (ptp-110) REVERT: C 276 GLN cc_start: 0.8442 (tt0) cc_final: 0.8106 (tm-30) REVERT: C 545 TRP cc_start: 0.8676 (m100) cc_final: 0.8470 (m-10) REVERT: C 602 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: C 681 ARG cc_start: 0.7186 (mmm-85) cc_final: 0.6679 (tpp80) REVERT: C 724 VAL cc_start: 0.7754 (OUTLIER) cc_final: 0.7460 (m) REVERT: N 11 LYS cc_start: 0.8550 (tttp) cc_final: 0.8248 (ptmt) REVERT: R 23 GLU cc_start: 0.6197 (mp0) cc_final: 0.5960 (mp0) REVERT: R 76 ASN cc_start: 0.8666 (m-40) cc_final: 0.7534 (t0) REVERT: R 88 LEU cc_start: 0.8686 (mm) cc_final: 0.8410 (mm) REVERT: D 8 LYS cc_start: 0.8532 (tttp) cc_final: 0.8315 (tmtt) REVERT: D 16 ASP cc_start: 0.7641 (m-30) cc_final: 0.7350 (t0) REVERT: D 63 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8599 (mmtp) REVERT: U 25 ASN cc_start: 0.8692 (m110) cc_final: 0.8341 (m110) REVERT: U 41 GLN cc_start: 0.7391 (mt0) cc_final: 0.7155 (mt0) outliers start: 45 outliers final: 25 residues processed: 265 average time/residue: 0.1076 time to fit residues: 42.2108 Evaluate side-chains 252 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 472 LEU Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 54 GLN 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 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 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 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.8980 chunk 100 optimal weight: 0.0370 chunk 90 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 615 ASN N 41 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098870 restraints weight = 26947.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099550 restraints weight = 19212.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100175 restraints weight = 17649.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102484 restraints weight = 12612.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102478 restraints weight = 9690.891| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 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 = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 12987 Z= 0.140 Angle : 0.592 9.643 17555 Z= 0.302 Chirality : 0.042 0.222 2004 Planarity : 0.003 0.049 2220 Dihedral : 4.353 60.271 1728 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.27 % Allowed : 22.84 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.21), residues: 1560 helix: 1.37 (0.19), residues: 724 sheet: -0.43 (0.36), residues: 207 loop : -2.18 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 118 TYR 0.013 0.001 TYR C 278 PHE 0.014 0.001 PHE S 14 TRP 0.020 0.001 TRP S 55 HIS 0.009 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00312 (12972) covalent geometry : angle 0.57797 (17542) SS BOND : bond 0.00454 ( 2) SS BOND : angle 5.38789 ( 4) hydrogen bonds : bond 0.04152 ( 664) hydrogen bonds : angle 4.61032 ( 1920) metal coordination : bond 0.04163 ( 11) metal coordination : angle 5.27162 ( 6) Misc. bond : bond 0.00030 ( 1) link_TRANS : bond 0.00507 ( 1) link_TRANS : angle 0.50264 ( 3) *********************** 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 264 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: T 223 MET cc_start: 0.8261 (mmm) cc_final: 0.7987 (mmp) REVERT: T 230 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7407 (mp0) REVERT: T 277 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7514 (tm-30) REVERT: T 322 ASP cc_start: 0.7826 (m-30) cc_final: 0.7530 (t70) REVERT: S 108 MET cc_start: 0.7595 (mtp) cc_final: 0.6797 (mmp) REVERT: S 122 ASN cc_start: 0.8454 (t0) cc_final: 0.8083 (t0) REVERT: C 147 ARG cc_start: 0.6310 (mmt90) cc_final: 0.4172 (mmt180) REVERT: C 188 GLU cc_start: 0.8711 (tp30) cc_final: 0.7779 (tp30) REVERT: C 191 ARG cc_start: 0.8194 (ptp-110) cc_final: 0.7887 (ptp-110) REVERT: C 276 GLN cc_start: 0.8443 (tt0) cc_final: 0.8077 (tm-30) REVERT: C 577 ARG cc_start: 0.6865 (ptt180) cc_final: 0.6369 (ptp-170) REVERT: C 613 GLN cc_start: 0.8191 (tp40) cc_final: 0.7613 (tt0) REVERT: C 681 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6553 (tpp80) REVERT: C 724 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7464 (m) REVERT: N 11 LYS cc_start: 0.8556 (tttp) cc_final: 0.8293 (ptmt) REVERT: R 76 ASN cc_start: 0.8646 (m-40) cc_final: 0.7515 (t0) REVERT: R 88 LEU cc_start: 0.8643 (mm) cc_final: 0.8427 (mm) REVERT: D 8 LYS cc_start: 0.8517 (tttp) cc_final: 0.8315 (tmtt) REVERT: D 16 ASP cc_start: 0.7766 (m-30) cc_final: 0.7389 (t0) REVERT: D 63 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8609 (mmtp) REVERT: U 25 ASN cc_start: 0.8684 (m110) cc_final: 0.8330 (m110) outliers start: 45 outliers final: 35 residues processed: 244 average time/residue: 0.1078 time to fit residues: 39.1884 Evaluate side-chains 244 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 478 LEU Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain S residue 121 PHE 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 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 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 77 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 114 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.126196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099056 restraints weight = 26990.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100209 restraints weight = 18988.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100710 restraints weight = 17120.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102777 restraints weight = 12308.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102718 restraints weight = 9643.649| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 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 = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 12987 Z= 0.137 Angle : 0.594 8.652 17555 Z= 0.304 Chirality : 0.042 0.241 2004 Planarity : 0.003 0.051 2220 Dihedral : 4.332 56.347 1728 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.27 % Allowed : 23.13 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1560 helix: 1.42 (0.19), residues: 724 sheet: -0.44 (0.36), residues: 208 loop : -2.08 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.014 0.001 TYR C 278 PHE 0.013 0.001 PHE C 606 TRP 0.031 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00303 (12972) covalent geometry : angle 0.58241 (17542) SS BOND : bond 0.00292 ( 2) SS BOND : angle 4.57851 ( 4) hydrogen bonds : bond 0.04086 ( 664) hydrogen bonds : angle 4.57377 ( 1920) metal coordination : bond 0.04343 ( 11) metal coordination : angle 5.26197 ( 6) Misc. bond : bond 0.00036 ( 1) link_TRANS : bond 0.00464 ( 1) link_TRANS : angle 0.29379 ( 3) *********************** 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 269 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8254 (mmm) cc_final: 0.7977 (mmp) REVERT: T 277 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7506 (tm-30) REVERT: T 322 ASP cc_start: 0.7820 (m-30) cc_final: 0.7512 (t70) REVERT: T 349 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8400 (pt) REVERT: S 55 TRP cc_start: 0.8401 (t60) cc_final: 0.7809 (t60) REVERT: S 122 ASN cc_start: 0.8401 (t0) cc_final: 0.8046 (t0) REVERT: C 147 ARG cc_start: 0.6452 (mmt90) cc_final: 0.4505 (mmt180) REVERT: C 188 GLU cc_start: 0.8725 (tp30) cc_final: 0.7743 (tp30) REVERT: C 191 ARG cc_start: 0.8071 (ptp-110) cc_final: 0.7752 (ptp-110) REVERT: C 276 GLN cc_start: 0.8417 (tt0) cc_final: 0.8025 (tm-30) REVERT: C 577 ARG cc_start: 0.6881 (ptt180) cc_final: 0.6388 (ptp-170) REVERT: C 608 MET cc_start: 0.6227 (mtm) cc_final: 0.5984 (mtt) REVERT: C 681 ARG cc_start: 0.7104 (mmm-85) cc_final: 0.6640 (tpp80) REVERT: C 724 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7424 (m) REVERT: N 11 LYS cc_start: 0.8619 (tttp) cc_final: 0.8374 (ptmt) REVERT: R 76 ASN cc_start: 0.8780 (m-40) cc_final: 0.7603 (t0) REVERT: D 8 LYS cc_start: 0.8546 (tttp) cc_final: 0.8327 (tmtt) REVERT: D 9 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7832 (tt0) REVERT: D 63 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8626 (mmtp) REVERT: U 15 LEU cc_start: 0.8547 (mm) cc_final: 0.8264 (mp) REVERT: U 25 ASN cc_start: 0.8680 (m110) cc_final: 0.8331 (m110) REVERT: U 49 GLN cc_start: 0.8655 (mm110) cc_final: 0.8390 (tp40) outliers start: 45 outliers final: 37 residues processed: 249 average time/residue: 0.1005 time to fit residues: 37.5908 Evaluate side-chains 246 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 349 LEU 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 479 VAL Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain S residue 121 PHE 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 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 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 148 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 147 optimal weight: 0.0070 chunk 154 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 388 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.128210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101239 restraints weight = 26692.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101894 restraints weight = 18657.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102651 restraints weight = 18284.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103702 restraints weight = 12323.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104094 restraints weight = 10877.644| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 12987 Z= 0.115 Angle : 0.595 7.818 17555 Z= 0.301 Chirality : 0.041 0.168 2004 Planarity : 0.003 0.040 2220 Dihedral : 4.271 55.574 1728 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.91 % Allowed : 23.93 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.21), residues: 1560 helix: 1.42 (0.19), residues: 733 sheet: -0.19 (0.36), residues: 216 loop : -2.13 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.012 0.001 TYR C 278 PHE 0.019 0.001 PHE S 14 TRP 0.029 0.002 TRP S 70 HIS 0.008 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00243 (12972) covalent geometry : angle 0.58656 (17542) SS BOND : bond 0.00543 ( 2) SS BOND : angle 3.37835 ( 4) hydrogen bonds : bond 0.03806 ( 664) hydrogen bonds : angle 4.48573 ( 1920) metal coordination : bond 0.04298 ( 11) metal coordination : angle 4.72822 ( 6) Misc. bond : bond 0.00036 ( 1) link_TRANS : bond 0.00376 ( 1) link_TRANS : angle 0.62087 ( 3) *********************** 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 278 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8181 (mmm) cc_final: 0.7931 (mmp) REVERT: T 277 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7505 (tm-30) REVERT: T 322 ASP cc_start: 0.7802 (m-30) cc_final: 0.7474 (t70) REVERT: T 349 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8407 (pt) REVERT: S 122 ASN cc_start: 0.8333 (t0) cc_final: 0.7976 (t0) REVERT: C 32 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.5898 (t80) REVERT: C 147 ARG cc_start: 0.6580 (mmt90) cc_final: 0.4458 (mmt180) REVERT: C 188 GLU cc_start: 0.8702 (tp30) cc_final: 0.7880 (tp30) REVERT: C 191 ARG cc_start: 0.8040 (ptp-110) cc_final: 0.7595 (ptp-110) REVERT: C 276 GLN cc_start: 0.8365 (tt0) cc_final: 0.8000 (tm-30) REVERT: C 577 ARG cc_start: 0.6759 (ptt180) cc_final: 0.6252 (ptp-170) REVERT: C 633 MET cc_start: 0.7567 (ppp) cc_final: 0.6210 (mmp) REVERT: C 681 ARG cc_start: 0.7119 (mmm-85) cc_final: 0.6617 (tpp80) REVERT: C 724 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7495 (m) REVERT: R 76 ASN cc_start: 0.8743 (m-40) cc_final: 0.7519 (t0) REVERT: D 16 ASP cc_start: 0.7665 (m-30) cc_final: 0.7229 (t0) REVERT: D 63 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8596 (mmtp) REVERT: D 66 LYS cc_start: 0.8625 (mttt) cc_final: 0.8229 (ttpt) REVERT: U 15 LEU cc_start: 0.8574 (mm) cc_final: 0.8281 (mp) REVERT: U 25 ASN cc_start: 0.8670 (m110) cc_final: 0.8326 (m110) REVERT: U 41 GLN cc_start: 0.6806 (mt0) cc_final: 0.6501 (mp10) REVERT: U 49 GLN cc_start: 0.8564 (mm110) cc_final: 0.8262 (tp40) outliers start: 40 outliers final: 29 residues processed: 266 average time/residue: 0.1048 time to fit residues: 41.0525 Evaluate side-chains 247 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 349 LEU 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 479 VAL Chi-restraints excluded: chain T residue 534 VAL Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 121 PHE 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 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 682 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.125461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098038 restraints weight = 26770.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099643 restraints weight = 18709.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100149 restraints weight = 16295.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.102245 restraints weight = 11779.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102180 restraints weight = 9104.732| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 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 = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 12987 Z= 0.166 Angle : 0.632 13.284 17555 Z= 0.320 Chirality : 0.043 0.165 2004 Planarity : 0.003 0.038 2220 Dihedral : 4.304 50.998 1728 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.05 % Allowed : 24.07 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.22), residues: 1560 helix: 1.43 (0.19), residues: 731 sheet: -0.23 (0.35), residues: 216 loop : -2.08 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 506 TYR 0.016 0.001 TYR C 278 PHE 0.020 0.001 PHE T 566 TRP 0.030 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00377 (12972) covalent geometry : angle 0.62403 (17542) SS BOND : bond 0.00459 ( 2) SS BOND : angle 3.68871 ( 4) hydrogen bonds : bond 0.04184 ( 664) hydrogen bonds : angle 4.57182 ( 1920) metal coordination : bond 0.04378 ( 11) metal coordination : angle 4.66553 ( 6) Misc. bond : bond 0.00002 ( 1) link_TRANS : bond 0.00208 ( 1) link_TRANS : angle 0.23288 ( 3) *********************** 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 256 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8145 (mmm) cc_final: 0.7863 (mmp) REVERT: T 277 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7574 (tm-30) REVERT: T 322 ASP cc_start: 0.7843 (m-30) cc_final: 0.7506 (t70) REVERT: T 349 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8458 (pt) REVERT: S 122 ASN cc_start: 0.8305 (t0) cc_final: 0.7976 (t0) REVERT: C 147 ARG cc_start: 0.6524 (mmt90) cc_final: 0.6172 (mtt-85) REVERT: C 276 GLN cc_start: 0.8416 (tt0) cc_final: 0.8030 (tm-30) REVERT: C 555 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6634 (tt) REVERT: C 577 ARG cc_start: 0.6844 (ptt180) cc_final: 0.6341 (ptp-170) REVERT: C 633 MET cc_start: 0.7581 (ppp) cc_final: 0.6194 (mmp) REVERT: C 681 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6633 (tpp80) REVERT: C 724 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7487 (m) REVERT: N 50 MET cc_start: 0.8734 (mmm) cc_final: 0.8203 (mtp) REVERT: R 76 ASN cc_start: 0.8825 (m-40) cc_final: 0.7630 (t0) REVERT: D 16 ASP cc_start: 0.7712 (m-30) cc_final: 0.7405 (t0) REVERT: D 63 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8603 (mmtp) REVERT: U 15 LEU cc_start: 0.8630 (mm) cc_final: 0.8353 (mp) REVERT: U 25 ASN cc_start: 0.8702 (m110) cc_final: 0.8344 (m110) outliers start: 42 outliers final: 35 residues processed: 240 average time/residue: 0.0989 time to fit residues: 35.5600 Evaluate side-chains 246 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 338 ILE Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 349 LEU 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 478 LEU Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 534 VAL Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain S residue 121 PHE 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 402 PHE 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 682 VAL 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 U residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 24 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 U 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098578 restraints weight = 26922.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099508 restraints weight = 19146.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100190 restraints weight = 18674.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101140 restraints weight = 12469.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101574 restraints weight = 11035.845| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | 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: 3 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 12987 Z= 0.148 Angle : 0.632 12.119 17555 Z= 0.320 Chirality : 0.043 0.179 2004 Planarity : 0.003 0.034 2220 Dihedral : 4.306 49.905 1728 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.84 % Allowed : 24.87 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1560 helix: 1.43 (0.19), residues: 729 sheet: -0.20 (0.36), residues: 216 loop : -2.09 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 506 TYR 0.014 0.001 TYR C 278 PHE 0.021 0.001 PHE S 14 TRP 0.045 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00334 (12972) covalent geometry : angle 0.62454 (17542) SS BOND : bond 0.00450 ( 2) SS BOND : angle 3.46080 ( 4) hydrogen bonds : bond 0.04121 ( 664) hydrogen bonds : angle 4.55788 ( 1920) metal coordination : bond 0.04409 ( 11) metal coordination : angle 4.48059 ( 6) Misc. bond : bond 0.00012 ( 1) link_TRANS : bond 0.00253 ( 1) link_TRANS : angle 0.23957 ( 3) ********************** 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 250 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8125 (mmm) cc_final: 0.7854 (mmp) REVERT: T 277 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7499 (tm-30) REVERT: T 322 ASP cc_start: 0.7806 (m-30) cc_final: 0.7521 (t70) REVERT: T 349 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8467 (pt) REVERT: T 357 ILE cc_start: 0.8680 (mt) cc_final: 0.8478 (mp) REVERT: S 55 TRP cc_start: 0.8325 (t60) cc_final: 0.7880 (t60) REVERT: S 122 ASN cc_start: 0.8304 (t0) cc_final: 0.7968 (t0) REVERT: C 147 ARG cc_start: 0.6479 (mmt90) cc_final: 0.6173 (mtt-85) REVERT: C 188 GLU cc_start: 0.8691 (tp30) cc_final: 0.7688 (tp30) REVERT: C 191 ARG cc_start: 0.8093 (ptp-110) cc_final: 0.7724 (ptp-110) REVERT: C 276 GLN cc_start: 0.8423 (tt0) cc_final: 0.8044 (tm-30) REVERT: C 555 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6606 (tt) REVERT: C 633 MET cc_start: 0.7626 (ppp) cc_final: 0.6152 (mmp) REVERT: C 681 ARG cc_start: 0.7162 (mmm-85) cc_final: 0.6638 (tpp80) REVERT: C 724 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7633 (m) REVERT: N 50 MET cc_start: 0.8721 (mmm) cc_final: 0.8094 (mtp) REVERT: R 23 GLU cc_start: 0.5586 (mp0) cc_final: 0.5377 (mp0) REVERT: R 76 ASN cc_start: 0.8800 (m-40) cc_final: 0.7614 (t0) REVERT: D 16 ASP cc_start: 0.7732 (m-30) cc_final: 0.7407 (t0) REVERT: D 63 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8580 (mmtp) REVERT: U 15 LEU cc_start: 0.8623 (mm) cc_final: 0.8358 (mp) REVERT: U 25 ASN cc_start: 0.8658 (m110) cc_final: 0.8287 (m110) REVERT: U 64 GLU cc_start: 0.7304 (mp0) cc_final: 0.7036 (pt0) outliers start: 39 outliers final: 34 residues processed: 236 average time/residue: 0.1078 time to fit residues: 38.1484 Evaluate side-chains 242 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 349 LEU 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 478 LEU Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 534 VAL Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 59 HIS 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 402 PHE 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 682 VAL 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 56 CYS 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 94 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 78 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 388 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN U 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097549 restraints weight = 26866.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098468 restraints weight = 19485.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098994 restraints weight = 18111.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101097 restraints weight = 12618.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101116 restraints weight = 9726.778| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 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 = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 12987 Z= 0.176 Angle : 0.642 11.918 17555 Z= 0.326 Chirality : 0.043 0.166 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.341 48.085 1728 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.20 % Allowed : 24.22 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.22), residues: 1560 helix: 1.41 (0.19), residues: 731 sheet: -0.25 (0.35), residues: 224 loop : -2.07 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 506 TYR 0.015 0.001 TYR C 278 PHE 0.020 0.001 PHE S 14 TRP 0.041 0.002 TRP S 55 HIS 0.007 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00405 (12972) covalent geometry : angle 0.63330 (17542) SS BOND : bond 0.00470 ( 2) SS BOND : angle 3.53414 ( 4) hydrogen bonds : bond 0.04278 ( 664) hydrogen bonds : angle 4.62092 ( 1920) metal coordination : bond 0.04171 ( 11) metal coordination : angle 4.91900 ( 6) Misc. bond : bond 0.00001 ( 1) link_TRANS : bond 0.00251 ( 1) link_TRANS : angle 0.14929 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.29 seconds wall clock time: 38 minutes 16.87 seconds (2296.87 seconds total)