Starting phenix.real_space_refine on Thu Sep 26 09:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/09_2024/6ttu_10585.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/09_2024/6ttu_10585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/09_2024/6ttu_10585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/09_2024/6ttu_10585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/09_2024/6ttu_10585.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/09_2024/6ttu_10585.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1 5.49 5 S 69 5.16 5 C 8099 2.51 5 N 2204 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12746 Number of models: 1 Model: "" Number of chains: 9 Chain: "T" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3085 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 891 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5728 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 688} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 666 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "D" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1135 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 58 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10515 SG CYS R 42 72.537 59.783 38.458 1.00105.69 S ATOM 10534 SG CYS R 45 71.727 62.144 41.587 1.00 96.79 S ATOM 10782 SG CYS R 83 74.603 62.879 39.323 1.00114.58 S ATOM 10711 SG CYS R 75 77.674 50.473 29.345 1.00132.51 S ATOM 10878 SG CYS R 94 78.374 51.519 33.079 1.00107.60 S ATOM 10601 SG CYS R 53 73.307 67.468 39.926 1.00145.22 S ATOM 10624 SG CYS R 56 72.428 70.984 38.455 1.00149.84 S ATOM 10661 SG CYS R 68 71.603 67.584 36.570 1.00150.04 S Time building chain proxies: 7.79, per 1000 atoms: 0.61 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=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 6 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 15 sheets defined 50.3% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'T' and resid 179 through 187 Proline residue: T 185 - end of helix Processing helix chain 'T' and resid 189 through 199 removed outlier: 3.724A pdb=" N TYR T 199 " --> pdb=" O ASN T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 210 Processing helix chain 'T' and resid 212 through 222 Processing helix chain 'T' and resid 223 through 236 Processing helix chain 'T' and resid 236 through 247 Processing helix chain 'T' and resid 248 through 252 Processing helix chain 'T' and resid 265 through 289 removed outlier: 3.929A pdb=" N ARG T 269 " --> pdb=" O ASN T 265 " (cutoff:3.500A) Proline residue: T 273 - end of helix Processing helix chain 'T' and resid 533 through 538 removed outlier: 3.697A pdb=" N ASP T 538 " --> pdb=" O VAL T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 542 through 545 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 31 Processing helix chain 'S' and resid 45 through 59 Processing helix chain 'S' and resid 69 through 76 Processing helix chain 'S' and resid 78 through 93 Processing helix chain 'S' and resid 94 through 108 Processing helix chain 'S' and resid 113 through 122 Processing helix chain 'S' and resid 131 through 138 Processing helix chain 'C' and resid 17 through 33 removed outlier: 3.846A pdb=" N THR C 33 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.781A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 Processing helix chain 'C' and resid 113 through 137 removed outlier: 3.827A pdb=" N LYS C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.024A pdb=" N VAL C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.880A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 252 removed outlier: 3.901A pdb=" N SER C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 278 removed outlier: 3.555A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 4.563A pdb=" N GLU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.747A pdb=" N GLN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.840A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 354 removed outlier: 3.575A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.921A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.973A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.737A pdb=" N LYS C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.624A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.601A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 525 removed outlier: 7.165A pdb=" N PHE C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 Processing helix chain 'C' and resid 604 through 614 Processing helix chain 'C' and resid 622 through 627 Processing helix chain 'C' and resid 632 through 645 removed outlier: 4.539A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 723 removed outlier: 4.431A pdb=" N LYS C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'N' and resid 22 through 32 removed outlier: 3.547A pdb=" N VAL N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 removed outlier: 3.627A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.758A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 112 removed outlier: 3.640A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 4.276A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.604A pdb=" N ARG D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 37 through 41 Processing helix chain 'U' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'T' and resid 308 through 311 removed outlier: 3.972A pdb=" N CYS T 308 " --> pdb=" O GLY T 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP T 329 " --> pdb=" O CYS T 335 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS T 335 " --> pdb=" O ASP T 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 346 through 351 removed outlier: 6.604A pdb=" N ASP T 369 " --> pdb=" O MET T 375 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET T 375 " --> pdb=" O ASP T 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 386 through 392 removed outlier: 6.396A pdb=" N ILE T 405 " --> pdb=" O VAL T 421 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL T 421 " --> pdb=" O ILE T 405 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL T 407 " --> pdb=" O ARG T 419 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP T 415 " --> pdb=" O ALA T 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 429 through 434 removed outlier: 3.806A pdb=" N SER T 443 " --> pdb=" O THR T 447 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR T 447 " --> pdb=" O SER T 443 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASN T 452 " --> pdb=" O PHE T 458 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE T 458 " --> pdb=" O ASN T 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 469 through 475 removed outlier: 3.666A pdb=" N ARG T 500 " --> pdb=" O LEU T 490 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP T 492 " --> pdb=" O CYS T 498 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N CYS T 498 " --> pdb=" O ASP T 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 509 through 514 removed outlier: 6.809A pdb=" N ASP T 532 " --> pdb=" O CYS T 547 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS T 547 " --> pdb=" O ASP T 532 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 560 through 563 Processing sheet with id=AA8, first strand: chain 'S' and resid 13 through 17 removed outlier: 9.556A pdb=" N VAL S 39 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LYS S 5 " --> pdb=" O VAL S 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 534 through 541 removed outlier: 3.661A pdb=" N ALA R 29 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 31 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU R 32 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 599 through 602 removed outlier: 3.573A pdb=" N VAL C 591 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU R 23 " --> pdb=" O VAL C 591 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 620 through 621 removed outlier: 3.902A pdb=" N TYR C 620 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 12 through 17 removed outlier: 8.689A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL N 70 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.599A pdb=" N SER D 22 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 35 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 12 through 16 664 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 3.89 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: 6996 17.93 - 35.85: 673 35.85 - 53.78: 136 53.78 - 71.71: 32 71.71 - 89.63: 14 Dihedral angle restraints: 7851 sinusoidal: 3146 harmonic: 4705 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 7848 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: 2220 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 2217 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 3 2.03 - 2.75: 1879 2.75 - 3.46: 18694 3.46 - 4.18: 28942 4.18 - 4.90: 51556 Nonbonded interactions: 101074 Sorted by model distance: nonbonded pdb=" NZ LYS C 720 " pdb=" C GLY N 76 " model vdw 1.312 3.350 nonbonded pdb=" C GLY U 75 " pdb=" N CYS I 20 " model vdw 1.336 3.350 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 ... (remaining 101069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.490 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- 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 : 0.006 0.095 12972 Z= 0.381 Angle : 0.880 10.205 17542 Z= 0.529 Chirality : 0.047 0.267 2004 Planarity : 0.004 0.056 2220 Dihedral : 15.099 89.634 4779 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.29 % Allowed : 7.85 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1560 helix: -0.55 (0.18), residues: 726 sheet: -1.63 (0.33), residues: 215 loop : -3.52 (0.20), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 368 HIS 0.027 0.002 HIS R 77 PHE 0.013 0.002 PHE C 508 TYR 0.017 0.002 TYR C 377 ARG 0.005 0.000 ARG C 506 *********************** 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 fitting. rotamer outliers: 4 poor density : 353 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8100 (mmm) cc_final: 0.7887 (mmp) REVERT: T 230 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7455 (mt-10) REVERT: T 277 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7523 (tm-30) REVERT: T 322 ASP cc_start: 0.7901 (m-30) cc_final: 0.7687 (t70) REVERT: T 440 VAL cc_start: 0.9051 (t) cc_final: 0.8835 (p) REVERT: T 581 ASP cc_start: 0.8785 (t70) cc_final: 0.8222 (p0) REVERT: S 13 ILE cc_start: 0.7421 (tp) cc_final: 0.7065 (tt) REVERT: S 48 ILE cc_start: 0.9131 (mp) cc_final: 0.8241 (mp) REVERT: S 108 MET cc_start: 0.7670 (mtp) cc_final: 0.6957 (mmp) REVERT: S 113 THR cc_start: 0.7942 (p) cc_final: 0.6983 (p) REVERT: S 122 ASN cc_start: 0.8611 (t0) cc_final: 0.8410 (t0) REVERT: C 147 ARG cc_start: 0.5345 (mmt180) cc_final: 0.3502 (mmt180) REVERT: C 188 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7979 (tm-30) REVERT: N 24 GLU cc_start: 0.8531 (tp30) cc_final: 0.8190 (tp30) REVERT: D 16 ASP cc_start: 0.7716 (m-30) cc_final: 0.7440 (t0) REVERT: D 63 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8742 (mmtp) outliers start: 4 outliers final: 1 residues processed: 357 average time/residue: 0.3101 time to fit residues: 151.2675 Evaluate side-chains 235 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 43 ASN S 59 HIS C 214 ASN C 308 GLN C 309 ASN C 602 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12972 Z= 0.218 Angle : 0.624 8.182 17542 Z= 0.330 Chirality : 0.043 0.228 2004 Planarity : 0.004 0.046 2220 Dihedral : 4.141 69.533 1729 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.82 % Allowed : 16.51 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1560 helix: 0.73 (0.19), residues: 728 sheet: -1.02 (0.35), residues: 213 loop : -2.91 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 248 HIS 0.010 0.001 HIS R 82 PHE 0.014 0.002 PHE C 95 TYR 0.022 0.002 TYR T 438 ARG 0.008 0.001 ARG T 234 *********************** 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 fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8149 (mmm) cc_final: 0.7867 (mmp) REVERT: T 230 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7476 (mt-10) REVERT: T 277 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7456 (tm-30) REVERT: T 322 ASP cc_start: 0.7912 (m-30) cc_final: 0.7698 (t70) REVERT: T 581 ASP cc_start: 0.8786 (t70) cc_final: 0.8313 (p0) REVERT: S 108 MET cc_start: 0.7611 (mtp) cc_final: 0.6847 (mmm) REVERT: S 116 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8017 (tt0) REVERT: S 122 ASN cc_start: 0.8657 (t0) cc_final: 0.8447 (t0) REVERT: C 147 ARG cc_start: 0.5365 (mmt180) cc_final: 0.3934 (mmt180) REVERT: C 681 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6552 (tpp80) REVERT: C 716 VAL cc_start: 0.8887 (p) cc_final: 0.8661 (p) REVERT: N 24 GLU cc_start: 0.8243 (tp30) cc_final: 0.7946 (tp30) REVERT: R 23 GLU cc_start: 0.5522 (mp0) cc_final: 0.5306 (mp0) REVERT: R 76 ASN cc_start: 0.8599 (m-40) cc_final: 0.7571 (t0) REVERT: D 16 ASP cc_start: 0.7666 (m-30) cc_final: 0.7435 (t0) REVERT: D 63 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8705 (mmtp) REVERT: D 112 ASP cc_start: 0.8126 (m-30) cc_final: 0.7589 (m-30) REVERT: U 25 ASN cc_start: 0.8698 (m110) cc_final: 0.8403 (m110) outliers start: 25 outliers final: 16 residues processed: 285 average time/residue: 0.2258 time to fit residues: 95.2394 Evaluate side-chains 242 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 226 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU 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 625 LEU Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 82 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 113 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12972 Z= 0.210 Angle : 0.591 7.055 17542 Z= 0.310 Chirality : 0.042 0.194 2004 Planarity : 0.004 0.040 2220 Dihedral : 4.368 66.947 1729 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.05 % Allowed : 18.91 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1560 helix: 1.05 (0.19), residues: 723 sheet: -0.80 (0.35), residues: 218 loop : -2.50 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 531 HIS 0.008 0.001 HIS R 82 PHE 0.017 0.001 PHE C 595 TYR 0.015 0.001 TYR T 251 ARG 0.013 0.001 ARG C 34 *********************** 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 288 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8171 (mmm) cc_final: 0.7943 (mmp) REVERT: T 277 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7426 (tm-30) REVERT: T 322 ASP cc_start: 0.7958 (m-30) cc_final: 0.7656 (t70) REVERT: S 14 PHE cc_start: 0.7544 (t80) cc_final: 0.7262 (t80) REVERT: S 84 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8038 (tm-30) REVERT: S 108 MET cc_start: 0.7603 (mtp) cc_final: 0.6713 (mmp) REVERT: S 116 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7994 (pt0) REVERT: S 122 ASN cc_start: 0.8598 (t0) cc_final: 0.8291 (t0) REVERT: C 147 ARG cc_start: 0.5540 (mmt180) cc_final: 0.3847 (mmt180) REVERT: C 187 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8334 (mt) REVERT: C 188 GLU cc_start: 0.8582 (tp30) cc_final: 0.7273 (tp30) REVERT: C 191 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7448 (ptp-110) REVERT: C 613 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7275 (tp40) REVERT: C 681 ARG cc_start: 0.6909 (mmm-85) cc_final: 0.6512 (tpp80) REVERT: C 724 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7624 (m) REVERT: N 24 GLU cc_start: 0.8199 (tp30) cc_final: 0.7852 (tp30) REVERT: R 76 ASN cc_start: 0.8637 (m-40) cc_final: 0.7615 (t0) REVERT: D 16 ASP cc_start: 0.7719 (m-30) cc_final: 0.7466 (t0) REVERT: D 63 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8623 (mmtp) REVERT: D 112 ASP cc_start: 0.7893 (m-30) cc_final: 0.7643 (m-30) REVERT: U 25 ASN cc_start: 0.8663 (m110) cc_final: 0.8360 (m110) outliers start: 42 outliers final: 28 residues processed: 267 average time/residue: 0.2297 time to fit residues: 90.3166 Evaluate side-chains 254 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 222 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 134 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12972 Z= 0.190 Angle : 0.575 9.939 17542 Z= 0.298 Chirality : 0.041 0.185 2004 Planarity : 0.003 0.063 2220 Dihedral : 4.376 65.959 1729 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.20 % Allowed : 19.64 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1560 helix: 1.13 (0.19), residues: 725 sheet: -0.69 (0.35), residues: 221 loop : -2.36 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 70 HIS 0.016 0.001 HIS S 59 PHE 0.010 0.001 PHE C 566 TYR 0.012 0.001 TYR C 278 ARG 0.006 0.000 ARG S 118 *********************** 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 292 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 248 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8228 (mmm) cc_final: 0.7987 (mmp) REVERT: T 230 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7362 (mp0) REVERT: T 277 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7479 (tm-30) REVERT: T 322 ASP cc_start: 0.7924 (m-30) cc_final: 0.7640 (t70) REVERT: T 478 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7832 (mm) REVERT: S 119 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8242 (mmtt) REVERT: S 122 ASN cc_start: 0.8528 (t0) cc_final: 0.8177 (t0) REVERT: C 147 ARG cc_start: 0.5713 (mmt180) cc_final: 0.3919 (mmt180) REVERT: C 187 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8316 (mt) REVERT: C 188 GLU cc_start: 0.8600 (tp30) cc_final: 0.7977 (tp30) REVERT: C 276 GLN cc_start: 0.8467 (tt0) cc_final: 0.8179 (tm-30) REVERT: C 540 LEU cc_start: 0.8995 (mt) cc_final: 0.8731 (mp) REVERT: C 681 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6631 (tpp80) REVERT: C 724 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7509 (m) REVERT: N 11 LYS cc_start: 0.8709 (tttp) cc_final: 0.8422 (ptmt) REVERT: N 24 GLU cc_start: 0.8170 (tp30) cc_final: 0.7822 (tp30) REVERT: R 23 GLU cc_start: 0.6160 (mp0) cc_final: 0.5774 (mp0) REVERT: R 76 ASN cc_start: 0.8594 (m-40) cc_final: 0.7519 (t0) REVERT: R 88 LEU cc_start: 0.8715 (mm) cc_final: 0.8408 (mm) REVERT: D 63 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8613 (mmtp) REVERT: D 112 ASP cc_start: 0.7950 (m-30) cc_final: 0.7531 (m-30) REVERT: U 25 ASN cc_start: 0.8671 (m110) cc_final: 0.8350 (m110) outliers start: 44 outliers final: 28 residues processed: 272 average time/residue: 0.2388 time to fit residues: 94.1490 Evaluate side-chains 253 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 478 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 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 D residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 388 HIS C 206 GLN C 284 GLN C 602 GLN ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12972 Z= 0.196 Angle : 0.571 7.809 17542 Z= 0.296 Chirality : 0.042 0.220 2004 Planarity : 0.003 0.052 2220 Dihedral : 4.371 63.111 1728 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.27 % Allowed : 21.24 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1560 helix: 1.26 (0.19), residues: 726 sheet: -0.52 (0.36), residues: 212 loop : -2.18 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 70 HIS 0.010 0.001 HIS R 82 PHE 0.014 0.001 PHE C 606 TYR 0.013 0.001 TYR C 278 ARG 0.005 0.000 ARG T 187 *********************** 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 276 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: T 223 MET cc_start: 0.8252 (mmm) cc_final: 0.8008 (mmp) REVERT: T 230 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7438 (mp0) REVERT: T 245 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8195 (ttm170) REVERT: T 277 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7501 (tm-30) REVERT: T 322 ASP cc_start: 0.7861 (m-30) cc_final: 0.7580 (t70) REVERT: S 108 MET cc_start: 0.7474 (mtp) cc_final: 0.6696 (mmp) REVERT: S 119 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8375 (mmtt) REVERT: S 122 ASN cc_start: 0.8418 (t0) cc_final: 0.8023 (t0) REVERT: C 147 ARG cc_start: 0.6120 (mmt90) cc_final: 0.4112 (mmt180) REVERT: C 188 GLU cc_start: 0.8619 (tp30) cc_final: 0.7969 (tp30) REVERT: C 276 GLN cc_start: 0.8494 (tt0) cc_final: 0.8190 (tm-30) REVERT: C 613 GLN cc_start: 0.8089 (tp40) cc_final: 0.7728 (tp40) REVERT: C 681 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6886 (tpp80) REVERT: C 724 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7410 (m) REVERT: R 76 ASN cc_start: 0.8681 (m-40) cc_final: 0.7536 (t0) REVERT: R 88 LEU cc_start: 0.8723 (mm) cc_final: 0.8435 (mm) REVERT: D 16 ASP cc_start: 0.7741 (m-30) cc_final: 0.7449 (t0) REVERT: U 25 ASN cc_start: 0.8661 (m110) cc_final: 0.8326 (m110) outliers start: 45 outliers final: 30 residues processed: 256 average time/residue: 0.2358 time to fit residues: 88.9713 Evaluate side-chains 250 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 472 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12972 Z= 0.177 Angle : 0.562 8.589 17542 Z= 0.291 Chirality : 0.041 0.237 2004 Planarity : 0.003 0.050 2220 Dihedral : 4.322 61.356 1728 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.05 % Allowed : 22.04 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1560 helix: 1.30 (0.19), residues: 734 sheet: -0.37 (0.36), residues: 205 loop : -2.20 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 55 HIS 0.009 0.001 HIS R 82 PHE 0.014 0.001 PHE C 606 TYR 0.013 0.001 TYR C 278 ARG 0.004 0.000 ARG U 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8246 (mmm) cc_final: 0.8006 (mmp) REVERT: T 230 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7429 (mp0) REVERT: T 245 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8292 (ttm110) REVERT: T 277 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7456 (tm-30) REVERT: T 322 ASP cc_start: 0.7854 (m-30) cc_final: 0.7568 (t70) REVERT: S 7 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7621 (pp30) REVERT: S 122 ASN cc_start: 0.8425 (t0) cc_final: 0.8065 (t0) REVERT: C 147 ARG cc_start: 0.6123 (mmt90) cc_final: 0.3977 (mmt180) REVERT: C 188 GLU cc_start: 0.8668 (tp30) cc_final: 0.8022 (tp30) REVERT: C 276 GLN cc_start: 0.8476 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 469 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7913 (mpp) REVERT: C 540 LEU cc_start: 0.8730 (mp) cc_final: 0.7284 (mp) REVERT: C 545 TRP cc_start: 0.8630 (m100) cc_final: 0.8104 (m-10) REVERT: C 577 ARG cc_start: 0.6853 (ptt180) cc_final: 0.6377 (ptp-170) REVERT: C 681 ARG cc_start: 0.7057 (mmm-85) cc_final: 0.6771 (tpp80) REVERT: C 724 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7492 (m) REVERT: N 11 LYS cc_start: 0.8594 (tttp) cc_final: 0.8345 (ptmt) REVERT: R 76 ASN cc_start: 0.8709 (m-40) cc_final: 0.7519 (t0) REVERT: R 88 LEU cc_start: 0.8673 (mm) cc_final: 0.8430 (mm) REVERT: D 12 ASP cc_start: 0.8255 (m-30) cc_final: 0.8036 (t0) REVERT: D 60 TYR cc_start: 0.8808 (t80) cc_final: 0.8584 (t80) REVERT: U 15 LEU cc_start: 0.8622 (mm) cc_final: 0.8349 (mp) REVERT: U 25 ASN cc_start: 0.8651 (m110) cc_final: 0.8313 (m110) outliers start: 42 outliers final: 32 residues processed: 257 average time/residue: 0.2405 time to fit residues: 90.7540 Evaluate side-chains 253 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 472 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 7 GLN Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 MET 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 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 D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 615 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12972 Z= 0.188 Angle : 0.570 7.910 17542 Z= 0.295 Chirality : 0.042 0.216 2004 Planarity : 0.003 0.048 2220 Dihedral : 4.303 59.446 1728 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.42 % Allowed : 22.76 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1560 helix: 1.34 (0.19), residues: 734 sheet: -0.33 (0.36), residues: 211 loop : -2.17 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 55 HIS 0.009 0.001 HIS R 82 PHE 0.013 0.001 PHE C 606 TYR 0.013 0.001 TYR C 278 ARG 0.003 0.000 ARG C 577 *********************** 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 277 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 230 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8202 (mmm) cc_final: 0.7936 (mmp) REVERT: T 245 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8290 (ttm110) REVERT: T 277 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7482 (tm-30) REVERT: T 322 ASP cc_start: 0.7795 (m-30) cc_final: 0.7518 (t70) REVERT: S 119 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8088 (mmtt) REVERT: S 122 ASN cc_start: 0.8370 (t0) cc_final: 0.8065 (t0) REVERT: C 147 ARG cc_start: 0.6102 (mmt90) cc_final: 0.4149 (mmt180) REVERT: C 188 GLU cc_start: 0.8681 (tp30) cc_final: 0.7948 (tp30) REVERT: C 276 GLN cc_start: 0.8497 (tt0) cc_final: 0.8165 (tm-30) REVERT: C 469 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7847 (mpp) REVERT: C 577 ARG cc_start: 0.6816 (ptt180) cc_final: 0.6336 (ptp-170) REVERT: C 681 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6736 (tpp80) REVERT: C 716 VAL cc_start: 0.8893 (p) cc_final: 0.8693 (p) REVERT: C 724 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7453 (m) REVERT: N 11 LYS cc_start: 0.8586 (tttp) cc_final: 0.8355 (ptmt) REVERT: R 76 ASN cc_start: 0.8774 (m-40) cc_final: 0.7568 (t0) REVERT: R 88 LEU cc_start: 0.8640 (mm) cc_final: 0.8438 (mm) REVERT: D 12 ASP cc_start: 0.8305 (m-30) cc_final: 0.8042 (t0) REVERT: D 60 TYR cc_start: 0.8832 (t80) cc_final: 0.8625 (t80) REVERT: U 15 LEU cc_start: 0.8646 (mm) cc_final: 0.8362 (mp) REVERT: U 25 ASN cc_start: 0.8663 (m110) cc_final: 0.8325 (m110) outliers start: 47 outliers final: 33 residues processed: 257 average time/residue: 0.2299 time to fit residues: 87.4571 Evaluate side-chains 256 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 245 ARG Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 98 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 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 MET 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 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 Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS C 214 ASN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12972 Z= 0.178 Angle : 0.582 8.163 17542 Z= 0.301 Chirality : 0.042 0.195 2004 Planarity : 0.003 0.046 2220 Dihedral : 4.299 57.988 1728 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.49 % Allowed : 23.05 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1560 helix: 1.40 (0.19), residues: 728 sheet: -0.24 (0.37), residues: 203 loop : -2.12 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP S 55 HIS 0.009 0.001 HIS R 82 PHE 0.023 0.001 PHE S 14 TYR 0.013 0.001 TYR C 278 ARG 0.003 0.000 ARG C 577 *********************** 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 283 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8199 (mmm) cc_final: 0.7997 (mmp) REVERT: T 230 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7410 (mp0) REVERT: T 277 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7456 (tm-30) REVERT: T 322 ASP cc_start: 0.7779 (m-30) cc_final: 0.7509 (t70) REVERT: S 119 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8095 (mmtt) REVERT: S 122 ASN cc_start: 0.8357 (t0) cc_final: 0.8039 (t0) REVERT: C 147 ARG cc_start: 0.6251 (mmt90) cc_final: 0.4097 (mmt180) REVERT: C 276 GLN cc_start: 0.8460 (tt0) cc_final: 0.8114 (tm-30) REVERT: C 469 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.7887 (mpp) REVERT: C 577 ARG cc_start: 0.6812 (ptt180) cc_final: 0.6306 (ptp-170) REVERT: C 633 MET cc_start: 0.7586 (ppp) cc_final: 0.6180 (mmp) REVERT: C 681 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.6707 (tpp80) REVERT: C 716 VAL cc_start: 0.8941 (p) cc_final: 0.8734 (p) REVERT: C 724 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7506 (m) REVERT: R 76 ASN cc_start: 0.8777 (m-40) cc_final: 0.7558 (t0) REVERT: D 12 ASP cc_start: 0.8333 (m-30) cc_final: 0.8022 (t0) REVERT: D 60 TYR cc_start: 0.8837 (t80) cc_final: 0.8604 (t80) REVERT: D 112 ASP cc_start: 0.8036 (m-30) cc_final: 0.7713 (m-30) REVERT: U 15 LEU cc_start: 0.8631 (mm) cc_final: 0.8371 (mp) outliers start: 48 outliers final: 38 residues processed: 259 average time/residue: 0.2387 time to fit residues: 89.6433 Evaluate side-chains 256 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 98 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 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 MET 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 686 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.0770 chunk 92 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12972 Z= 0.184 Angle : 0.602 9.006 17542 Z= 0.309 Chirality : 0.042 0.186 2004 Planarity : 0.003 0.049 2220 Dihedral : 4.223 55.629 1728 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.13 % Allowed : 24.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1560 helix: 1.41 (0.19), residues: 727 sheet: -0.20 (0.37), residues: 201 loop : -2.06 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 PHE 0.010 0.001 PHE C 95 TYR 0.013 0.001 TYR C 278 ARG 0.003 0.000 ARG D 136 *********************** 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 260 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8156 (mmm) cc_final: 0.7950 (mmp) REVERT: T 277 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7466 (tm-30) REVERT: T 322 ASP cc_start: 0.7783 (m-30) cc_final: 0.7508 (t70) REVERT: S 55 TRP cc_start: 0.8299 (t60) cc_final: 0.7913 (t60) REVERT: S 119 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8120 (mmtt) REVERT: S 122 ASN cc_start: 0.8322 (t0) cc_final: 0.8005 (t0) REVERT: C 188 GLU cc_start: 0.8662 (tp30) cc_final: 0.7697 (tp30) REVERT: C 191 ARG cc_start: 0.7920 (ptp-110) cc_final: 0.7613 (ptp-110) REVERT: C 276 GLN cc_start: 0.8436 (tt0) cc_final: 0.8096 (tm-30) REVERT: C 469 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: C 633 MET cc_start: 0.7573 (ppp) cc_final: 0.6158 (mmp) REVERT: C 681 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6707 (tpp80) REVERT: C 716 VAL cc_start: 0.8941 (p) cc_final: 0.8725 (p) REVERT: R 76 ASN cc_start: 0.8786 (m-40) cc_final: 0.7579 (t0) REVERT: D 12 ASP cc_start: 0.8415 (m-30) cc_final: 0.8080 (t0) REVERT: D 112 ASP cc_start: 0.8028 (m-30) cc_final: 0.7778 (m-30) REVERT: U 15 LEU cc_start: 0.8604 (mm) cc_final: 0.8342 (mp) outliers start: 43 outliers final: 38 residues processed: 240 average time/residue: 0.2275 time to fit residues: 81.1613 Evaluate side-chains 253 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 59 HIS 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 C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 MET 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 686 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain U residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 0.0570 chunk 143 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 191 HIS T 388 HIS ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12972 Z= 0.183 Angle : 0.623 12.651 17542 Z= 0.315 Chirality : 0.042 0.186 2004 Planarity : 0.003 0.043 2220 Dihedral : 4.203 53.420 1728 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.05 % Allowed : 24.00 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1560 helix: 1.43 (0.19), residues: 727 sheet: -0.04 (0.37), residues: 205 loop : -1.99 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 PHE 0.026 0.001 PHE S 14 TYR 0.013 0.001 TYR C 278 ARG 0.004 0.000 ARG C 577 ********************** 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 263 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: T 277 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7533 (tm-30) REVERT: T 322 ASP cc_start: 0.7785 (m-30) cc_final: 0.7504 (t70) REVERT: S 55 TRP cc_start: 0.8290 (t60) cc_final: 0.7950 (t60) REVERT: S 119 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8091 (mmtt) REVERT: S 122 ASN cc_start: 0.8319 (t0) cc_final: 0.7995 (t0) REVERT: C 191 ARG cc_start: 0.7948 (ptp-110) cc_final: 0.7618 (ptp-110) REVERT: C 276 GLN cc_start: 0.8433 (tt0) cc_final: 0.8084 (tm-30) REVERT: C 469 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7839 (mpp) REVERT: C 555 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6625 (tt) REVERT: C 577 ARG cc_start: 0.6747 (ptt180) cc_final: 0.6306 (ptp-170) REVERT: C 633 MET cc_start: 0.7544 (ppp) cc_final: 0.6147 (mmp) REVERT: C 681 ARG cc_start: 0.6950 (mmm-85) cc_final: 0.6708 (tpp80) REVERT: C 716 VAL cc_start: 0.8907 (p) cc_final: 0.8680 (p) REVERT: R 23 GLU cc_start: 0.5591 (mp0) cc_final: 0.4927 (mp0) REVERT: R 76 ASN cc_start: 0.8775 (m-40) cc_final: 0.7548 (t0) REVERT: D 12 ASP cc_start: 0.8349 (m-30) cc_final: 0.8140 (t70) REVERT: D 66 LYS cc_start: 0.8550 (mttt) cc_final: 0.8237 (ttpt) REVERT: U 15 LEU cc_start: 0.8562 (mm) cc_final: 0.8302 (mp) REVERT: U 49 GLN cc_start: 0.8630 (mm110) cc_final: 0.8291 (tp40) outliers start: 42 outliers final: 37 residues processed: 243 average time/residue: 0.2368 time to fit residues: 84.6854 Evaluate side-chains 249 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 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 59 HIS Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 98 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 145 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 MET 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 611 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain U residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.127485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100274 restraints weight = 26699.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101457 restraints weight = 18989.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102176 restraints weight = 17632.095| |-----------------------------------------------------------------------------| 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: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12972 Z= 0.198 Angle : 0.646 12.576 17542 Z= 0.327 Chirality : 0.043 0.196 2004 Planarity : 0.003 0.042 2220 Dihedral : 4.264 51.241 1728 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.27 % Allowed : 24.00 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1560 helix: 1.44 (0.19), residues: 724 sheet: -0.16 (0.36), residues: 207 loop : -1.98 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 55 HIS 0.012 0.001 HIS T 191 PHE 0.013 0.001 PHE T 566 TYR 0.014 0.001 TYR C 278 ARG 0.006 0.000 ARG C 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.05 seconds wall clock time: 51 minutes 22.02 seconds (3082.02 seconds total)