Starting phenix.real_space_refine (version: dev) on Fri Sep 2 08:38:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7z_27240/09_2022/8d7z_27240_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.001 sd= 0.061 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 202 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ASP 925": "OD1" <-> "OD2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/modules/chem_data/mon_lib" Total number of atoms: 11228 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8039 Classifications: {'peptide': 1132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 841 Unresolved non-hydrogen angles: 1067 Unresolved non-hydrogen dihedrals: 660 Unresolved non-hydrogen chiralities: 102 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': 24, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 416 Chain: "B" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2944 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 360} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 201 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {' ZN': 1, 'QFC': 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 10207 SG CYS B 323 44.077 88.915 31.267 1.00236.30 S ATOM 10223 SG CYS B 326 43.485 92.561 30.483 1.00238.80 S ATOM 10721 SG CYS B 391 43.064 89.721 27.543 1.00218.80 S ATOM 10740 SG CYS B 394 45.934 91.290 28.641 1.00228.55 S ATOM 11016 SG CYS C 147 56.933 86.307 20.559 1.00216.63 S Time building chain proxies: 6.85, per 1000 atoms: 0.61 Number of scatterers: 11228 At special positions: 0 Unit cell: (90.85, 110.4, 158.7, 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 2 29.99 S 59 16.00 F 1 9.00 O 2120 8.00 N 1942 7.00 C 7104 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: 4.42 Conformation dependent library (CDL) restraints added in 1.9 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 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 163 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 167 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 147 " Number of angles added : 6 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 28 sheets defined 10.3% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' 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 1059 Processing helix chain 'A' and resid 1070 through 1074 Processing helix chain 'A' and resid 1091 through 1097 removed outlier: 3.713A pdb=" N PHE A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1108 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.645A 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: 4.011A pdb=" N HIS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASN B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.659A 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 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: 7.222A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.677A 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: 5.918A 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: 6.381A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 104 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER A 94 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.044A 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 removed outlier: 3.510A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 177 through 184 Processing sheet with id= F, first strand: chain 'A' and resid 218 through 221 Processing sheet with id= G, first strand: chain 'A' and resid 258 through 263 removed outlier: 7.147A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.999A pdb=" N GLY A 325 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 314 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE A 323 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TYR A 316 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 321 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 351 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.907A 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 removed outlier: 3.547A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.530A pdb=" N THR A 424 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.768A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 470 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 498 through 503 removed outlier: 7.143A pdb=" N ALA A 511 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA A 501 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 509 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N CYS A 503 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 530 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLN A 528 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 611 through 613 removed outlier: 4.061A pdb=" N LYS A 627 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.566A pdb=" N CYS A 652 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 678 through 682 removed outlier: 3.652A pdb=" N GLY A 702 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 701 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 400 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 749 through 751 removed outlier: 6.541A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.858A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 862 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 870 through 876 removed outlier: 7.067A pdb=" N SER A 883 " --> pdb=" O TYR A 871 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET A 873 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 881 " --> pdb=" O MET A 873 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 875 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 920 through 923 removed outlier: 3.661A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS A 936 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 942 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.511A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.399A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 566 through 569 removed outlier: 3.748A pdb=" N HIS A 578 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 588 through 595 removed outlier: 6.901A pdb=" N ALA A 605 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE A 591 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 603 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A 593 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 6.149A 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: 6.362A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.191A 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: 3.873A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 171 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 169 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 96 through 100 Processing sheet with id= AA, first strand: chain 'B' and resid 346 through 350 Processing sheet with id= AB, first strand: chain 'B' and resid 368 through 371 removed outlier: 3.718A pdb=" N VAL B 388 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 385 " --> pdb=" O THR B 403 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 867 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: 5.12 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1921 1.28 - 1.42: 2779 1.42 - 1.55: 6662 1.55 - 1.69: 0 1.69 - 1.83: 86 Bond restraints: 11448 Sorted by residual: bond pdb=" C25 QFC B 502 " pdb=" N3 QFC B 502 " ideal model delta sigma weight residual 1.481 1.369 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C26 QFC B 502 " pdb=" N3 QFC B 502 " ideal model delta sigma weight residual 1.479 1.372 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C2 QFC B 502 " pdb=" C31 QFC B 502 " ideal model delta sigma weight residual 1.535 1.441 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C19 QFC B 502 " pdb=" N2 QFC B 502 " ideal model delta sigma weight residual 1.446 1.360 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C18 QFC B 502 " pdb=" C19 QFC B 502 " ideal model delta sigma weight residual 1.546 1.480 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 11443 not shown) Histogram of bond angle deviations from ideal: 98.79 - 114.69: 7083 114.69 - 130.58: 8475 130.58 - 146.47: 45 146.47 - 162.37: 0 162.37 - 178.26: 1 Bond angle restraints: 15604 Sorted by residual: angle pdb=" C5 QFC B 502 " pdb=" C QFC B 502 " pdb=" F QFC B 502 " ideal model delta sigma weight residual 141.69 118.14 23.55 3.00e+00 1.11e-01 6.16e+01 angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.25 111.06 -7.81 1.05e+00 9.07e-01 5.54e+01 angle pdb=" C1 QFC B 502 " pdb=" C QFC B 502 " pdb=" F QFC B 502 " ideal model delta sigma weight residual 98.22 118.17 -19.95 3.00e+00 1.11e-01 4.42e+01 angle pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sigma weight residual 111.26 101.60 9.66 1.66e+00 3.63e-01 3.39e+01 angle pdb=" N QFC B 502 " pdb=" C5 QFC B 502 " pdb=" C QFC B 502 " ideal model delta sigma weight residual 104.42 119.52 -15.10 3.00e+00 1.11e-01 2.53e+01 ... (remaining 15599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 6631 32.37 - 64.75: 169 64.75 - 97.12: 14 97.12 - 129.50: 0 129.50 - 161.87: 1 Dihedral angle restraints: 6815 sinusoidal: 2355 harmonic: 4460 Sorted by residual: dihedral pdb=" C CYS C 150 " pdb=" N CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta harmonic sigma weight residual -122.60 -109.06 -13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" O QFC B 502 " pdb=" C12 QFC B 502 " pdb=" C13 QFC B 502 " pdb=" C11 QFC B 502 " ideal model delta sinusoidal sigma weight residual 272.51 110.64 161.87 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N CYS C 150 " pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta harmonic sigma weight residual 122.80 112.71 10.09 0 2.50e+00 1.60e-01 1.63e+01 ... (remaining 6812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1587 0.072 - 0.144: 214 0.144 - 0.216: 3 0.216 - 0.288: 2 0.288 - 0.360: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA CYS C 150 " pdb=" N CYS C 150 " pdb=" C CYS C 150 " pdb=" CB CYS C 150 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C22 QFC B 502 " pdb=" C23 QFC B 502 " pdb=" C26 QFC B 502 " pdb=" N2 QFC B 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.31 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1804 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N QFC B 502 " 0.034 2.00e-02 2.50e+03 5.02e-02 6.29e+01 pdb=" C QFC B 502 " -0.046 2.00e-02 2.50e+03 pdb=" C1 QFC B 502 " -0.092 2.00e-02 2.50e+03 pdb=" C2 QFC B 502 " -0.054 2.00e-02 2.50e+03 pdb=" C3 QFC B 502 " -0.006 2.00e-02 2.50e+03 pdb=" C31 QFC B 502 " 0.012 2.00e-02 2.50e+03 pdb=" C4 QFC B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C5 QFC B 502 " -0.003 2.00e-02 2.50e+03 pdb=" F QFC B 502 " 0.072 2.00e-02 2.50e+03 pdb=" N4 QFC B 502 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 QFC B 502 " 0.025 2.00e-02 2.50e+03 3.94e-02 3.10e+01 pdb=" C11 QFC B 502 " 0.027 2.00e-02 2.50e+03 pdb=" C12 QFC B 502 " 0.015 2.00e-02 2.50e+03 pdb=" C13 QFC B 502 " -0.068 2.00e-02 2.50e+03 pdb=" C27 QFC B 502 " 0.027 2.00e-02 2.50e+03 pdb=" C28 QFC B 502 " 0.026 2.00e-02 2.50e+03 pdb=" C8 QFC B 502 " -0.067 2.00e-02 2.50e+03 pdb=" C9 QFC B 502 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O QFC B 502 " 0.030 2.00e-02 2.50e+03 2.82e-02 2.39e+01 pdb=" C14 QFC B 502 " -0.011 2.00e-02 2.50e+03 pdb=" C15 QFC B 502 " 0.005 2.00e-02 2.50e+03 pdb=" C16 QFC B 502 " 0.019 2.00e-02 2.50e+03 pdb=" C17 QFC B 502 " 0.016 2.00e-02 2.50e+03 pdb=" C18 QFC B 502 " -0.011 2.00e-02 2.50e+03 pdb=" C19 QFC B 502 " -0.012 2.00e-02 2.50e+03 pdb=" C20 QFC B 502 " -0.049 2.00e-02 2.50e+03 pdb=" C21 QFC B 502 " -0.026 2.00e-02 2.50e+03 pdb=" C22 QFC B 502 " 0.065 2.00e-02 2.50e+03 pdb=" N2 QFC B 502 " -0.014 2.00e-02 2.50e+03 pdb=" O1 QFC B 502 " -0.011 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1081 2.75 - 3.29: 10744 3.29 - 3.82: 17744 3.82 - 4.36: 20919 4.36 - 4.90: 37784 Nonbonded interactions: 88272 Sorted by model distance: nonbonded pdb=" OE2 GLU A 811 " pdb=" OG1 THR A 833 " model vdw 2.210 2.440 nonbonded pdb=" CB CYS C 150 " pdb="ZN ZN C 201 " model vdw 2.237 2.630 nonbonded pdb=" O GLY A1010 " pdb=" OG SER A1027 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 757 " pdb=" OD1 ASN A 790 " model vdw 2.252 2.440 nonbonded pdb=" OE2 GLU A 277 " pdb=" NH1 ARG A 279 " model vdw 2.259 2.520 ... (remaining 88267 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 59 5.16 5 C 7104 2.51 5 N 1942 2.21 5 O 2120 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 0.480 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: 0.010 Extract box with map and model: 3.370 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 36.340 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.112 11448 Z= 0.259 Angle : 0.689 23.546 15604 Z= 0.351 Chirality : 0.047 0.360 1807 Planarity : 0.004 0.091 2043 Dihedral : 14.564 161.869 3935 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.47 % Favored : 93.08 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.33 % 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: -2.00 (0.21), residues: 1531 helix: 0.18 (0.39), residues: 182 sheet: -1.14 (0.22), residues: 561 loop : -1.82 (0.21), residues: 788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 1.387 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 163 average time/residue: 0.2492 time to fit residues: 58.3492 Evaluate side-chains 120 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1119 time to fit residues: 2.0842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 61 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN B 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11448 Z= 0.151 Angle : 0.507 5.928 15604 Z= 0.264 Chirality : 0.044 0.149 1807 Planarity : 0.004 0.063 2043 Dihedral : 6.012 125.826 1648 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.34 % Favored : 93.27 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.93 (0.21), residues: 1531 helix: -0.01 (0.39), residues: 194 sheet: -0.94 (0.22), residues: 543 loop : -1.86 (0.20), residues: 794 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.334 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 0.2442 time to fit residues: 46.1663 Evaluate side-chains 126 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1189 time to fit residues: 3.5684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.3980 chunk 43 optimal weight: 50.0000 chunk 115 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 990 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.051 11448 Z= 0.504 Angle : 0.673 9.464 15604 Z= 0.343 Chirality : 0.049 0.245 1807 Planarity : 0.004 0.054 2043 Dihedral : 6.470 125.896 1648 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.71 % Favored : 91.97 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.26 (0.20), residues: 1531 helix: -0.05 (0.38), residues: 184 sheet: -1.23 (0.21), residues: 581 loop : -2.06 (0.20), residues: 766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.426 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 127 average time/residue: 0.2450 time to fit residues: 45.0711 Evaluate side-chains 121 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1074 time to fit residues: 3.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 132 optimal weight: 0.0060 chunk 39 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 HIS B 357 HIS C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11448 Z= 0.149 Angle : 0.492 6.182 15604 Z= 0.256 Chirality : 0.044 0.150 1807 Planarity : 0.003 0.045 2043 Dihedral : 5.999 122.788 1648 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.81 % Favored : 93.93 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.03 (0.21), residues: 1531 helix: 0.23 (0.40), residues: 184 sheet: -1.16 (0.21), residues: 582 loop : -1.86 (0.21), residues: 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.365 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.2428 time to fit residues: 44.7739 Evaluate side-chains 122 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1094 time to fit residues: 2.5345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 61 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 11448 Z= 0.370 Angle : 0.590 8.053 15604 Z= 0.303 Chirality : 0.047 0.184 1807 Planarity : 0.004 0.046 2043 Dihedral : 6.163 119.481 1648 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.38 % Favored : 92.36 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.11 (0.21), residues: 1531 helix: 0.06 (0.39), residues: 185 sheet: -1.14 (0.21), residues: 578 loop : -1.97 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.2358 time to fit residues: 46.0797 Evaluate side-chains 120 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1187 time to fit residues: 3.4769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 77 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS ** B 412 GLN ** 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: 0.7622 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11448 Z= 0.171 Angle : 0.496 6.162 15604 Z= 0.258 Chirality : 0.044 0.151 1807 Planarity : 0.003 0.044 2043 Dihedral : 5.861 116.534 1648 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.79 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.99 (0.21), residues: 1531 helix: 0.22 (0.39), residues: 188 sheet: -1.06 (0.21), residues: 586 loop : -1.91 (0.21), residues: 757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 129 average time/residue: 0.2414 time to fit residues: 45.1126 Evaluate side-chains 123 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1082 time to fit residues: 3.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 147 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.0040 chunk 91 optimal weight: 1.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 357 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11448 Z= 0.198 Angle : 0.510 7.253 15604 Z= 0.263 Chirality : 0.044 0.147 1807 Planarity : 0.003 0.044 2043 Dihedral : 5.755 112.927 1648 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.73 % Favored : 93.14 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.97 (0.21), residues: 1531 helix: 0.25 (0.40), residues: 188 sheet: -1.04 (0.21), residues: 586 loop : -1.90 (0.21), residues: 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 124 average time/residue: 0.2477 time to fit residues: 44.7254 Evaluate side-chains 121 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1068 time to fit residues: 2.7969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 28 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** 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: 0.7620 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11448 Z= 0.180 Angle : 0.495 6.312 15604 Z= 0.256 Chirality : 0.044 0.146 1807 Planarity : 0.003 0.044 2043 Dihedral : 5.623 108.888 1648 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.53 % Favored : 93.34 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.92 (0.21), residues: 1531 helix: 0.35 (0.40), residues: 188 sheet: -1.04 (0.21), residues: 594 loop : -1.86 (0.21), residues: 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 127 average time/residue: 0.2440 time to fit residues: 45.0579 Evaluate side-chains 121 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1130 time to fit residues: 2.7016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 11448 Z= 0.420 Angle : 0.615 8.381 15604 Z= 0.314 Chirality : 0.047 0.190 1807 Planarity : 0.004 0.046 2043 Dihedral : 5.901 105.069 1648 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.36 % Favored : 91.44 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.17 (0.20), residues: 1531 helix: 0.18 (0.39), residues: 185 sheet: -1.27 (0.21), residues: 597 loop : -1.96 (0.21), residues: 749 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.340 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 124 average time/residue: 0.2567 time to fit residues: 46.1764 Evaluate side-chains 125 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1209 time to fit residues: 3.6611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 101 optimal weight: 0.0170 chunk 152 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11448 Z= 0.163 Angle : 0.514 10.285 15604 Z= 0.263 Chirality : 0.044 0.151 1807 Planarity : 0.003 0.044 2043 Dihedral : 5.558 102.455 1648 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.97 (0.21), residues: 1531 helix: 0.37 (0.40), residues: 185 sheet: -1.11 (0.21), residues: 593 loop : -1.88 (0.21), residues: 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.328 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2579 time to fit residues: 44.9867 Evaluate side-chains 120 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.0170 chunk 121 optimal weight: 9.9990 chunk 50 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121290 restraints weight = 14846.965| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.31 r_work: 0.3413 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work: 0.3376 rms_B_bonded: 2.19 restraints_weight: 0.1250 r_work: 0.3351 rms_B_bonded: 2.39 restraints_weight: 0.0625 r_work: 0.3318 rms_B_bonded: 2.74 restraints_weight: 0.0312 r_work: 0.3274 rms_B_bonded: 3.31 restraints_weight: 0.0156 r_work: 0.3210 rms_B_bonded: 4.29 restraints_weight: 0.0078 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11448 Z= 0.176 Angle : 0.510 9.477 15604 Z= 0.260 Chirality : 0.044 0.148 1807 Planarity : 0.003 0.044 2043 Dihedral : 5.399 97.901 1648 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.12 % Favored : 92.75 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.90 (0.21), residues: 1531 helix: 0.39 (0.40), residues: 187 sheet: -1.03 (0.21), residues: 594 loop : -1.86 (0.21), residues: 750 =============================================================================== Job complete usr+sys time: 2093.63 seconds wall clock time: 38 minutes 54.83 seconds (2334.83 seconds total)