Starting phenix.real_space_refine on Thu Feb 15 07:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d80_27241/02_2024/8d80_27241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d80_27241/02_2024/8d80_27241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d80_27241/02_2024/8d80_27241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d80_27241/02_2024/8d80_27241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d80_27241/02_2024/8d80_27241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d80_27241/02_2024/8d80_27241_updated.pdb" } resolution = 3.6 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= -0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 226 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 59 5.16 5 C 7105 2.51 5 N 1944 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A GLU 892": "OE1" <-> "OE2" Residue "A GLU 898": "OE1" <-> "OE2" Residue "A ASP 963": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11230 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8028 Classifications: {'peptide': 1132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1081 Unresolved non-hydrogen dihedrals: 668 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 18, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 424 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2942 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 360} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8W7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10198 SG CYS B 323 45.349 122.008 54.411 1.00192.50 S ATOM 10218 SG CYS B 326 46.815 124.353 51.854 1.00195.77 S ATOM 10708 SG CYS B 391 45.263 125.795 55.152 1.00187.34 S ATOM 10727 SG CYS B 394 43.154 124.531 52.447 1.00195.38 S ATOM 11027 SG CYS C 147 30.359 128.003 59.238 1.00246.80 S Time building chain proxies: 6.58, per 1000 atoms: 0.59 Number of scatterers: 11230 At special positions: 0 Unit cell: (94.3, 148.35, 112.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 59 16.00 O 2120 8.00 N 1944 7.00 C 7105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.11 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 167 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 163 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 147 " Number of angles added : 6 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 29 sheets defined 10.8% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 986 through 989 No H-bonds generated for 'chain 'A' and resid 986 through 989' Processing helix chain 'A' and resid 1045 through 1060 removed outlier: 4.324A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1074 Processing helix chain 'A' and resid 1091 through 1099 removed outlier: 3.652A pdb=" N PHE A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1108 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.516A pdb=" N GLU A1135 " --> pdb=" O LYS A1131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1136 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A1139 " --> pdb=" O GLU A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.905A pdb=" N HIS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.782A pdb=" N TYR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'C' and resid 158 through 167 Processing sheet with id= A, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 7.131A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 18 through 21 removed outlier: 5.822A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 61 through 67 removed outlier: 6.425A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER A 94 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 121 through 124 Processing sheet with id= E, first strand: chain 'A' and resid 187 through 194 removed outlier: 3.674A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.505A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.937A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.558A pdb=" N LEU A 333 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 351 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 362 through 365 Processing sheet with id= J, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.633A pdb=" N THR A 424 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 476 through 480 removed outlier: 3.650A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 498 through 503 removed outlier: 6.920A pdb=" N ALA A 511 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA A 501 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 509 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N CYS A 503 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLN A 528 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.281A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 569 " --> pdb=" O CYS A 556 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 610 through 612 Processing sheet with id= O, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= P, first strand: chain 'A' and resid 678 through 682 removed outlier: 6.693A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 749 through 751 removed outlier: 3.520A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.629A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 862 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 873 through 876 removed outlier: 3.677A pdb=" N CYS A 903 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 913 through 917 Processing sheet with id= U, first strand: chain 'A' and resid 933 through 936 removed outlier: 3.581A pdb=" N LYS A 936 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.695A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 996 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 588 through 595 removed outlier: 6.983A pdb=" N ALA A 605 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 591 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 603 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N MET A 593 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR A 601 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.529A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.867A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 183 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG B 164 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 134 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA B 124 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY B 136 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 122 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 138 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE B 120 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 96 through 101 removed outlier: 3.610A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 320 through 322 removed outlier: 4.181A pdb=" N SER B 320 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.666A pdb=" N ALA B 347 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 368 through 371 removed outlier: 3.939A pdb=" N VAL B 388 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 385 " --> pdb=" O THR B 403 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 924 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: 4.54 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3451 1.33 - 1.46: 1913 1.46 - 1.58: 6000 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 11450 Sorted by residual: bond pdb=" N ASP B 75 " pdb=" CA ASP B 75 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.21e+00 bond pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.18e-02 7.18e+03 6.84e+00 bond pdb=" N LEU A 770 " pdb=" CA LEU A 770 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.38e+00 bond pdb=" N LYS B 324 " pdb=" CA LYS B 324 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.94e+00 bond pdb=" N SER B 77 " pdb=" CA SER B 77 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.84e+00 ... (remaining 11445 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.14: 253 106.14 - 113.11: 6231 113.11 - 120.09: 3730 120.09 - 127.07: 5273 127.07 - 134.04: 118 Bond angle restraints: 15605 Sorted by residual: angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.63e+01 angle pdb=" N ASP A1116 " pdb=" CA ASP A1116 " pdb=" C ASP A1116 " ideal model delta sigma weight residual 113.18 104.58 8.60 1.21e+00 6.83e-01 5.05e+01 angle pdb=" N LEU A1112 " pdb=" CA LEU A1112 " pdb=" C LEU A1112 " ideal model delta sigma weight residual 113.19 106.19 7.00 1.19e+00 7.06e-01 3.46e+01 angle pdb=" N LEU A 770 " pdb=" CA LEU A 770 " pdb=" C LEU A 770 " ideal model delta sigma weight residual 113.02 106.20 6.82 1.20e+00 6.94e-01 3.23e+01 angle pdb=" C GLN B 325 " pdb=" N CYS B 326 " pdb=" CA CYS B 326 " ideal model delta sigma weight residual 120.75 127.26 -6.51 1.51e+00 4.39e-01 1.86e+01 ... (remaining 15600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 6654 33.62 - 67.25: 150 67.25 - 100.87: 20 100.87 - 134.49: 5 134.49 - 168.11: 1 Dihedral angle restraints: 6830 sinusoidal: 2363 harmonic: 4467 Sorted by residual: dihedral pdb=" C19 8W7 B 502 " pdb=" C20 8W7 B 502 " pdb=" C21 8W7 B 502 " pdb=" N3 8W7 B 502 " ideal model delta sinusoidal sigma weight residual 46.78 -145.11 -168.11 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C22 8W7 B 502 " pdb=" C23 8W7 B 502 " pdb=" O5 8W7 B 502 " pdb=" C24 8W7 B 502 " ideal model delta sinusoidal sigma weight residual 57.07 -64.18 121.25 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C11 8W7 B 502 " pdb=" C10 8W7 B 502 " pdb=" C9 8W7 B 502 " pdb=" C13 8W7 B 502 " ideal model delta sinusoidal sigma weight residual -53.05 55.22 -108.27 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 6827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1406 0.049 - 0.098: 287 0.098 - 0.147: 106 0.147 - 0.196: 6 0.196 - 0.245: 2 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA TYR A1114 " pdb=" N TYR A1114 " pdb=" C TYR A1114 " pdb=" CB TYR A1114 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLN B 325 " pdb=" N GLN B 325 " pdb=" C GLN B 325 " pdb=" CB GLN B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU A 770 " pdb=" N LEU A 770 " pdb=" C LEU A 770 " pdb=" CB LEU A 770 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 1804 not shown) Planarity restraints: 2045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 8W7 B 502 " -0.175 2.00e-02 2.50e+03 1.93e-01 1.12e+03 pdb=" C2 8W7 B 502 " -0.111 2.00e-02 2.50e+03 pdb=" C3 8W7 B 502 " 0.022 2.00e-02 2.50e+03 pdb=" C4 8W7 B 502 " -0.106 2.00e-02 2.50e+03 pdb=" C5 8W7 B 502 " 0.026 2.00e-02 2.50e+03 pdb=" C6 8W7 B 502 " 0.091 2.00e-02 2.50e+03 pdb=" C7 8W7 B 502 " 0.231 2.00e-02 2.50e+03 pdb=" C8 8W7 B 502 " 0.120 2.00e-02 2.50e+03 pdb=" C9 8W7 B 502 " -0.460 2.00e-02 2.50e+03 pdb=" N1 8W7 B 502 " -0.041 2.00e-02 2.50e+03 pdb=" O1 8W7 B 502 " 0.307 2.00e-02 2.50e+03 pdb=" O4 8W7 B 502 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 8W7 B 502 " -0.013 2.00e-02 2.50e+03 4.88e-02 2.97e+01 pdb=" C12 8W7 B 502 " -0.009 2.00e-02 2.50e+03 pdb=" C13 8W7 B 502 " 0.058 2.00e-02 2.50e+03 pdb=" N2 8W7 B 502 " -0.080 2.00e-02 2.50e+03 pdb=" O3 8W7 B 502 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 766 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C SER A 766 " -0.053 2.00e-02 2.50e+03 pdb=" O SER A 766 " 0.020 2.00e-02 2.50e+03 pdb=" N SER A 767 " 0.018 2.00e-02 2.50e+03 ... (remaining 2042 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1078 2.75 - 3.29: 10591 3.29 - 3.82: 17396 3.82 - 4.36: 20347 4.36 - 4.90: 37228 Nonbonded interactions: 86640 Sorted by model distance: nonbonded pdb=" OD2 ASP B 265 " pdb=" OG SER B 339 " model vdw 2.212 2.440 nonbonded pdb=" CB CYS C 150 " pdb="ZN ZN C 201 " model vdw 2.281 2.630 nonbonded pdb=" NZ LYS A1081 " pdb=" OE2 GLU A1083 " model vdw 2.282 2.520 nonbonded pdb=" O ILE B 301 " pdb=" NH1 ARG B 307 " model vdw 2.287 2.520 nonbonded pdb=" O LEU A 356 " pdb=" OG SER A 379 " model vdw 2.300 2.440 ... (remaining 86635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 2.980 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.480 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.004 0.052 11450 Z= 0.249 Angle : 0.633 9.484 15605 Z= 0.371 Chirality : 0.046 0.245 1807 Planarity : 0.006 0.193 2045 Dihedral : 15.295 168.114 3946 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.67 % Favored : 93.74 % Rotamer: Outliers : 0.75 % Allowed : 0.57 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.72 (0.21), residues: 1534 helix: 0.12 (0.40), residues: 182 sheet: -0.77 (0.22), residues: 587 loop : -1.74 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.003 0.001 HIS A 789 PHE 0.013 0.001 PHE A1030 TYR 0.010 0.001 TYR B 227 ARG 0.006 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8666 (ptp) cc_final: 0.8401 (ptm) REVERT: A 782 PHE cc_start: 0.8393 (t80) cc_final: 0.8160 (t80) REVERT: B 194 MET cc_start: 0.8280 (tpp) cc_final: 0.7996 (mmm) outliers start: 8 outliers final: 1 residues processed: 105 average time/residue: 0.2128 time to fit residues: 34.1303 Evaluate side-chains 69 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 119 optimal weight: 0.3980 chunk 46 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 138 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 908 ASN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11450 Z= 0.398 Angle : 0.590 7.723 15605 Z= 0.306 Chirality : 0.045 0.150 1807 Planarity : 0.004 0.045 2045 Dihedral : 8.896 169.425 1665 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.39 % Favored : 93.35 % Rotamer: Outliers : 1.32 % Allowed : 6.97 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.64 (0.21), residues: 1534 helix: 0.27 (0.41), residues: 180 sheet: -0.68 (0.22), residues: 586 loop : -1.73 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.010 0.001 HIS B 397 PHE 0.015 0.002 PHE A1030 TYR 0.013 0.002 TYR A 42 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8649 (ptp) cc_final: 0.8271 (ptm) REVERT: B 64 MET cc_start: 0.5230 (tpp) cc_final: 0.4874 (tpt) REVERT: B 363 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6720 (m-80) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.2015 time to fit residues: 25.1319 Evaluate side-chains 76 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 50.0000 chunk 115 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 908 ASN A 993 GLN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11450 Z= 0.380 Angle : 0.564 6.318 15605 Z= 0.293 Chirality : 0.044 0.178 1807 Planarity : 0.004 0.044 2045 Dihedral : 8.370 169.631 1662 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.58 % Favored : 93.16 % Rotamer: Outliers : 1.70 % Allowed : 9.90 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.68 (0.21), residues: 1534 helix: 0.27 (0.40), residues: 181 sheet: -0.75 (0.22), residues: 582 loop : -1.74 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.010 0.001 HIS B 397 PHE 0.016 0.002 PHE A1030 TYR 0.012 0.001 TYR A 91 ARG 0.003 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.8871 (tpp) cc_final: 0.8580 (ttm) REVERT: A 1036 MET cc_start: 0.8867 (ptm) cc_final: 0.8591 (ppp) REVERT: B 387 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7344 (p) outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 0.1842 time to fit residues: 24.7625 Evaluate side-chains 79 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11450 Z= 0.148 Angle : 0.488 7.809 15605 Z= 0.251 Chirality : 0.044 0.299 1807 Planarity : 0.003 0.044 2045 Dihedral : 7.581 167.133 1662 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.00 % Favored : 93.74 % Rotamer: Outliers : 1.32 % Allowed : 12.16 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.53 (0.21), residues: 1534 helix: 0.28 (0.40), residues: 190 sheet: -0.68 (0.22), residues: 593 loop : -1.60 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 PHE 0.016 0.001 PHE A 782 TYR 0.010 0.001 TYR A 42 ARG 0.003 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8524 (ptp) cc_final: 0.8277 (ptm) REVERT: A 954 MET cc_start: 0.8772 (ttt) cc_final: 0.8493 (ttt) REVERT: A 1036 MET cc_start: 0.8832 (ptm) cc_final: 0.8590 (ppp) REVERT: B 288 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9154 (mp) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.1914 time to fit residues: 23.3954 Evaluate side-chains 74 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 126 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN A1034 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11450 Z= 0.294 Angle : 0.529 13.682 15605 Z= 0.269 Chirality : 0.044 0.309 1807 Planarity : 0.003 0.045 2045 Dihedral : 7.240 166.169 1662 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.58 % Favored : 93.16 % Rotamer: Outliers : 1.70 % Allowed : 12.63 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.53 (0.21), residues: 1534 helix: 0.18 (0.39), residues: 196 sheet: -0.64 (0.22), residues: 583 loop : -1.61 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 PHE 0.014 0.001 PHE A1030 TYR 0.016 0.001 TYR B 221 ARG 0.002 0.000 ARG A1074 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8656 (ptp) cc_final: 0.8375 (ptm) REVERT: A 1036 MET cc_start: 0.8863 (ptm) cc_final: 0.8628 (ppp) REVERT: B 288 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9212 (mp) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.2041 time to fit residues: 25.6318 Evaluate side-chains 77 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11450 Z= 0.471 Angle : 0.596 12.328 15605 Z= 0.306 Chirality : 0.046 0.288 1807 Planarity : 0.004 0.044 2045 Dihedral : 6.665 163.300 1662 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.04 % Favored : 92.70 % Rotamer: Outliers : 2.26 % Allowed : 13.20 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.65 (0.21), residues: 1534 helix: 0.00 (0.38), residues: 196 sheet: -0.67 (0.22), residues: 556 loop : -1.69 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 207 HIS 0.010 0.001 HIS B 397 PHE 0.015 0.002 PHE A1030 TYR 0.014 0.002 TYR A 91 ARG 0.003 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 62 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.8727 (ttt) cc_final: 0.8503 (ttt) REVERT: A 1036 MET cc_start: 0.8878 (ptm) cc_final: 0.8656 (ppp) outliers start: 24 outliers final: 18 residues processed: 82 average time/residue: 0.1827 time to fit residues: 24.4894 Evaluate side-chains 80 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11450 Z= 0.175 Angle : 0.483 11.868 15605 Z= 0.249 Chirality : 0.044 0.260 1807 Planarity : 0.003 0.044 2045 Dihedral : 6.177 160.729 1662 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.13 % Favored : 93.61 % Rotamer: Outliers : 1.60 % Allowed : 14.61 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.54 (0.21), residues: 1534 helix: 0.32 (0.39), residues: 196 sheet: -0.74 (0.22), residues: 586 loop : -1.58 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 PHE 0.011 0.001 PHE A1030 TYR 0.009 0.001 TYR B 227 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8568 (ptp) cc_final: 0.8300 (ptm) REVERT: A 1036 MET cc_start: 0.8862 (ptm) cc_final: 0.8629 (ppp) REVERT: B 288 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9164 (mp) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.1849 time to fit residues: 22.9904 Evaluate side-chains 75 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 134 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11450 Z= 0.183 Angle : 0.490 11.467 15605 Z= 0.248 Chirality : 0.043 0.250 1807 Planarity : 0.003 0.043 2045 Dihedral : 6.000 160.616 1662 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.13 % Favored : 93.61 % Rotamer: Outliers : 1.60 % Allowed : 15.17 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.48 (0.21), residues: 1534 helix: 0.37 (0.39), residues: 196 sheet: -0.70 (0.22), residues: 586 loop : -1.54 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.007 0.001 HIS B 397 PHE 0.012 0.001 PHE A1030 TYR 0.008 0.001 TYR A 42 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8600 (ptp) cc_final: 0.8342 (ptm) REVERT: A 1036 MET cc_start: 0.8849 (ptm) cc_final: 0.8615 (ppp) REVERT: B 194 MET cc_start: 0.8594 (mmm) cc_final: 0.8392 (mmm) REVERT: B 288 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9156 (mp) REVERT: B 363 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.7266 (m-80) outliers start: 17 outliers final: 12 residues processed: 72 average time/residue: 0.1855 time to fit residues: 22.0644 Evaluate side-chains 76 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 107 optimal weight: 0.0070 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11450 Z= 0.178 Angle : 0.477 11.207 15605 Z= 0.242 Chirality : 0.043 0.229 1807 Planarity : 0.003 0.043 2045 Dihedral : 5.791 160.367 1662 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.13 % Favored : 93.68 % Rotamer: Outliers : 1.41 % Allowed : 15.36 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.42 (0.21), residues: 1534 helix: 0.46 (0.39), residues: 196 sheet: -0.64 (0.22), residues: 583 loop : -1.53 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.006 0.001 HIS B 397 PHE 0.012 0.001 PHE A1030 TYR 0.008 0.001 TYR A 42 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.8576 (ptp) cc_final: 0.8318 (ptm) REVERT: A 1036 MET cc_start: 0.8847 (ptm) cc_final: 0.8611 (ppp) REVERT: B 194 MET cc_start: 0.8663 (mmm) cc_final: 0.8370 (mmm) REVERT: B 288 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9114 (mp) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.1960 time to fit residues: 22.8826 Evaluate side-chains 73 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 152 optimal weight: 0.0470 chunk 140 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11450 Z= 0.275 Angle : 0.517 11.000 15605 Z= 0.263 Chirality : 0.044 0.223 1807 Planarity : 0.003 0.043 2045 Dihedral : 5.891 160.545 1662 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.19 % Favored : 93.61 % Rotamer: Outliers : 1.51 % Allowed : 15.46 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.45 (0.21), residues: 1534 helix: 0.44 (0.39), residues: 196 sheet: -0.70 (0.22), residues: 584 loop : -1.52 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.007 0.001 HIS B 397 PHE 0.014 0.001 PHE A1030 TYR 0.010 0.001 TYR A 91 ARG 0.008 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.8653 (ptp) cc_final: 0.8412 (ptm) REVERT: A 1036 MET cc_start: 0.8866 (ptm) cc_final: 0.8631 (ppp) REVERT: B 194 MET cc_start: 0.8664 (mmm) cc_final: 0.8395 (mmm) REVERT: B 288 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9201 (mp) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.1935 time to fit residues: 22.1514 Evaluate side-chains 73 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 50 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.089413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.061136 restraints weight = 30921.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063726 restraints weight = 15425.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065350 restraints weight = 10318.754| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11450 Z= 0.314 Angle : 0.538 11.045 15605 Z= 0.274 Chirality : 0.044 0.225 1807 Planarity : 0.003 0.042 2045 Dihedral : 6.001 160.719 1662 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.32 % Favored : 93.42 % Rotamer: Outliers : 1.41 % Allowed : 15.65 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.51 (0.21), residues: 1534 helix: 0.35 (0.39), residues: 197 sheet: -0.75 (0.22), residues: 585 loop : -1.54 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 PHE 0.014 0.001 PHE A1030 TYR 0.011 0.001 TYR A 91 ARG 0.007 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.23 seconds wall clock time: 35 minutes 55.05 seconds (2155.05 seconds total)