Starting phenix.real_space_refine (version: dev) on Fri Sep 2 07:21:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234_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/8d7u_27234/09_2022/8d7u_27234_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7u_27234/09_2022/8d7u_27234_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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A ASP 986": "OD1" <-> "OD2" Residue "A GLU 1045": "OE1" <-> "OE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 313": "OD1" <-> "OD2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 377": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/modules/chem_data/mon_lib" Total number of atoms: 11072 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8047 Classifications: {'peptide': 1132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 832 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 653 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 404 Chain: "B" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3025 Unusual residues: {' ZN': 1, 'QFC': 1} Classifications: {'peptide': 384, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 362, None: 2} Not linked: pdbres="THR B 425 " pdbres=" ZN B 501 " Not linked: pdbres=" ZN B 501 " pdbres="QFC B 502 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 66 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10247 SG CYS B 323 41.560 88.680 30.907 1.00 70.87 S ATOM 10263 SG CYS B 326 40.281 91.785 29.926 1.00 84.79 S ATOM 10767 SG CYS B 391 38.772 89.022 27.622 1.00 79.10 S ATOM 10786 SG CYS B 394 42.362 90.125 27.496 1.00 91.19 S Time building chain proxies: 6.97, per 1000 atoms: 0.63 Number of scatterers: 11072 At special positions: 0 Unit cell: (89.7, 109.25, 157.55, 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 1 29.99 S 57 16.00 F 1 9.00 O 2097 8.00 N 1907 7.00 C 7009 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: 4.43 Conformation dependent library (CDL) restraints added in 2.2 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 " Number of angles added : 6 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 27 sheets defined 9.6% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 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 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' 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 1073 No H-bonds generated for 'chain 'A' and resid 1070 through 1073' Processing helix chain 'A' and resid 1091 through 1099 removed outlier: 3.664A pdb=" N PHE A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.720A 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: 3.886A pdb=" N ILE A1139 " --> pdb=" O GLU A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 233 through 236 removed outlier: 3.671A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 242 through 247 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 sheet with id= A, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 7.007A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 3.749A 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: 5.899A 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: 6.671A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER A 94 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.173A 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: 3.903A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.299A 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: 3.636A 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: 6.911A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.767A 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 317 removed outlier: 6.978A pdb=" N GLY A 325 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 314 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 323 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR A 316 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 321 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 333 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.960A 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: 3.658A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 410 through 413 Processing sheet with id= K, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.815A pdb=" N SER A 488 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.171A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.802A 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: 6.334A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 568 " --> pdb=" O HIS A 578 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS A 570 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 576 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 627 through 630 removed outlier: 4.378A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 604 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 594 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 637 through 640 Processing sheet with id= P, first strand: chain 'A' and resid 678 through 680 removed outlier: 6.581A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.572A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.715A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN A 845 " --> pdb=" O MET A 835 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.248A 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 875 removed outlier: 3.600A pdb=" N CYS A 903 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.603A 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 916 removed outlier: 3.613A pdb=" N TYR A 913 " --> pdb=" O GLY A 924 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.631A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 930 through 936 removed outlier: 3.623A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS A 936 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE A 942 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.732A pdb=" N ILE B 81 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 180 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 96 through 101 removed outlier: 3.563A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 320 through 322 removed outlier: 4.041A pdb=" N SER B 320 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.837A pdb=" N ALA B 347 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 368 through 371 removed outlier: 4.115A pdb=" N VAL B 388 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 403 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 933 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: 4.84 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: 1901 1.28 - 1.41: 2731 1.41 - 1.54: 6572 1.54 - 1.68: 6 1.68 - 1.81: 84 Bond restraints: 11294 Sorted by residual: bond pdb=" C LEU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.332 1.402 -0.070 1.12e-02 7.97e+03 3.93e+01 bond pdb=" C GLU A 842 " pdb=" N PRO A 843 " ideal model delta sigma weight residual 1.332 1.411 -0.079 1.34e-02 5.57e+03 3.48e+01 bond pdb=" C25 QFC B 502 " pdb=" N3 QFC B 502 " ideal model delta sigma weight residual 1.481 1.367 0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C26 QFC B 502 " pdb=" N3 QFC B 502 " ideal model delta sigma weight residual 1.479 1.369 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C GLU A1083 " pdb=" N PRO A1084 " ideal model delta sigma weight residual 1.331 1.392 -0.062 1.31e-02 5.83e+03 2.21e+01 ... (remaining 11289 not shown) Histogram of bond angle deviations from ideal: 97.33 - 113.55: 6524 113.55 - 129.76: 8813 129.76 - 145.98: 65 145.98 - 162.19: 0 162.19 - 178.41: 1 Bond angle restraints: 15403 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 141.69 118.49 23.20 3.00e+00 1.11e-01 5.98e+01 angle pdb=" N ASN B 203 " pdb=" CA ASN B 203 " pdb=" C ASN B 203 " ideal model delta sigma weight residual 113.18 103.44 9.74 1.33e+00 5.65e-01 5.36e+01 angle pdb=" N SER B 52 " pdb=" CA SER B 52 " pdb=" C SER B 52 " ideal model delta sigma weight residual 114.75 105.66 9.09 1.26e+00 6.30e-01 5.20e+01 angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.15 109.99 -6.84 9.70e-01 1.06e+00 4.98e+01 angle pdb=" C1 QFC B 502 " pdb=" C QFC B 502 " pdb=" F QFC B 502 " ideal model delta sigma weight residual 98.22 118.46 -20.24 3.00e+00 1.11e-01 4.55e+01 ... (remaining 15398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 6511 32.69 - 65.38: 188 65.38 - 98.07: 17 98.07 - 130.76: 0 130.76 - 163.45: 1 Dihedral angle restraints: 6717 sinusoidal: 2319 harmonic: 4398 Sorted by residual: dihedral pdb=" CA ASP B 117 " pdb=" C ASP B 117 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C ASN B 203 " pdb=" N ASN B 203 " pdb=" CA ASN B 203 " pdb=" CB ASN B 203 " ideal model delta harmonic sigma weight residual -122.60 -108.72 -13.88 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C ARG A 391 " pdb=" N ARG A 391 " pdb=" CA ARG A 391 " pdb=" CB ARG A 391 " ideal model delta harmonic sigma weight residual -122.60 -110.39 -12.21 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 6714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1526 0.080 - 0.159: 221 0.159 - 0.239: 23 0.239 - 0.318: 9 0.318 - 0.398: 3 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CA ARG A 391 " pdb=" N ARG A 391 " pdb=" C ARG A 391 " pdb=" CB ARG A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA ASN B 203 " pdb=" N ASN B 203 " pdb=" C ASN B 203 " pdb=" CB ASN B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA GLU A 842 " pdb=" N GLU A 842 " pdb=" C GLU A 842 " pdb=" CB GLU A 842 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1779 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O QFC B 502 " 0.017 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" C14 QFC B 502 " 0.007 2.00e-02 2.50e+03 pdb=" C15 QFC B 502 " -0.032 2.00e-02 2.50e+03 pdb=" C16 QFC B 502 " -0.048 2.00e-02 2.50e+03 pdb=" C17 QFC B 502 " -0.023 2.00e-02 2.50e+03 pdb=" C18 QFC B 502 " 0.019 2.00e-02 2.50e+03 pdb=" C19 QFC B 502 " 0.035 2.00e-02 2.50e+03 pdb=" C20 QFC B 502 " 0.041 2.00e-02 2.50e+03 pdb=" C21 QFC B 502 " 0.031 2.00e-02 2.50e+03 pdb=" C22 QFC B 502 " -0.120 2.00e-02 2.50e+03 pdb=" N2 QFC B 502 " 0.016 2.00e-02 2.50e+03 pdb=" O1 QFC B 502 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 915 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C LYS A 915 " 0.073 2.00e-02 2.50e+03 pdb=" O LYS A 915 " -0.027 2.00e-02 2.50e+03 pdb=" N THR A 916 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 326 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C CYS B 326 " -0.066 2.00e-02 2.50e+03 pdb=" O CYS B 326 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN B 327 " 0.022 2.00e-02 2.50e+03 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1136 2.75 - 3.28: 10358 3.28 - 3.82: 17418 3.82 - 4.36: 20815 4.36 - 4.90: 37214 Nonbonded interactions: 86941 Sorted by model distance: nonbonded pdb=" O PHE B 338 " pdb=" OG1 THR B 361 " model vdw 2.207 2.440 nonbonded pdb=" OG SER B 320 " pdb=" OG1 THR B 425 " model vdw 2.209 2.440 nonbonded pdb=" NZ LYS A1121 " pdb=" OD2 ASP A1128 " model vdw 2.215 2.520 nonbonded pdb=" NE2 GLN A 727 " pdb=" OG1 THR A 827 " model vdw 2.215 2.520 nonbonded pdb=" O SER A1071 " pdb=" OG SER A1075 " model vdw 2.216 2.440 ... (remaining 86936 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 1 6.06 5 S 57 5.16 5 C 7009 2.51 5 N 1907 2.21 5 O 2097 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: 0.010 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 36.650 Find NCS groups from input model: 0.340 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.114 11294 Z= 0.405 Angle : 0.934 23.196 15403 Z= 0.567 Chirality : 0.059 0.398 1782 Planarity : 0.005 0.047 2020 Dihedral : 15.299 163.451 3877 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.41 % Favored : 90.79 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.28 % 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: -2.12 (0.22), residues: 1510 helix: -0.21 (0.41), residues: 169 sheet: -0.80 (0.23), residues: 593 loop : -2.22 (0.21), residues: 748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 216 average time/residue: 0.2338 time to fit residues: 71.0555 Evaluate side-chains 145 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1380 time to fit residues: 4.7294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.0670 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN B 68 HIS B 203 ASN B 206 GLN B 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11294 Z= 0.171 Angle : 0.558 7.703 15403 Z= 0.289 Chirality : 0.045 0.160 1782 Planarity : 0.004 0.042 2020 Dihedral : 6.371 151.172 1624 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.62 % Favored : 92.98 % Rotamer Outliers : 0.76 % 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: -1.91 (0.22), residues: 1510 helix: 0.17 (0.40), residues: 176 sheet: -0.73 (0.23), residues: 599 loop : -2.10 (0.21), residues: 735 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.174 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 138 average time/residue: 0.2197 time to fit residues: 44.4477 Evaluate side-chains 122 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.363 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1160 time to fit residues: 3.1756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN B 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11294 Z= 0.268 Angle : 0.572 6.767 15403 Z= 0.294 Chirality : 0.045 0.152 1782 Planarity : 0.004 0.044 2020 Dihedral : 6.269 143.841 1624 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.82 % Favored : 92.78 % Rotamer Outliers : 1.14 % 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: -1.91 (0.22), residues: 1510 helix: 0.24 (0.41), residues: 175 sheet: -0.76 (0.22), residues: 606 loop : -2.10 (0.21), residues: 729 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.282 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.2197 time to fit residues: 40.4174 Evaluate side-chains 119 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1058 time to fit residues: 3.3262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11294 Z= 0.293 Angle : 0.575 6.489 15403 Z= 0.296 Chirality : 0.046 0.153 1782 Planarity : 0.004 0.044 2020 Dihedral : 6.142 135.605 1624 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.82 % Favored : 92.72 % Rotamer Outliers : 1.33 % 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: -1.92 (0.22), residues: 1510 helix: 0.20 (0.40), residues: 175 sheet: -0.74 (0.22), residues: 601 loop : -2.12 (0.21), residues: 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.2277 time to fit residues: 44.7469 Evaluate side-chains 122 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1153 time to fit residues: 3.6456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11294 Z= 0.224 Angle : 0.535 6.617 15403 Z= 0.276 Chirality : 0.044 0.150 1782 Planarity : 0.004 0.043 2020 Dihedral : 5.931 132.695 1624 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.29 % Favored : 93.25 % Rotamer Outliers : 0.76 % 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: -1.88 (0.22), residues: 1510 helix: 0.33 (0.41), residues: 176 sheet: -0.79 (0.22), residues: 615 loop : -2.05 (0.22), residues: 719 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.094 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.2214 time to fit residues: 41.5688 Evaluate side-chains 120 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1137 time to fit residues: 2.9001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.0270 chunk 131 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11294 Z= 0.213 Angle : 0.529 6.380 15403 Z= 0.271 Chirality : 0.044 0.149 1782 Planarity : 0.004 0.042 2020 Dihedral : 5.852 131.282 1624 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.09 % Favored : 93.44 % Rotamer Outliers : 0.67 % 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: -1.83 (0.22), residues: 1510 helix: 0.43 (0.41), residues: 176 sheet: -0.73 (0.22), residues: 604 loop : -2.06 (0.21), residues: 730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.170 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 125 average time/residue: 0.2112 time to fit residues: 39.9401 Evaluate side-chains 125 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1193 time to fit residues: 2.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN A1015 GLN A1055 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 11294 Z= 0.325 Angle : 0.595 7.874 15403 Z= 0.303 Chirality : 0.046 0.175 1782 Planarity : 0.004 0.043 2020 Dihedral : 6.056 131.047 1624 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.29 % Favored : 93.31 % Rotamer Outliers : 0.95 % 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: -1.92 (0.22), residues: 1510 helix: 0.23 (0.40), residues: 176 sheet: -0.80 (0.22), residues: 613 loop : -2.09 (0.22), residues: 721 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.369 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.2103 time to fit residues: 39.6450 Evaluate side-chains 118 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1211 time to fit residues: 2.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 chunk 114 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11294 Z= 0.189 Angle : 0.518 6.383 15403 Z= 0.267 Chirality : 0.044 0.145 1782 Planarity : 0.003 0.042 2020 Dihedral : 5.733 127.852 1624 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.09 % Favored : 93.51 % Rotamer Outliers : 0.57 % 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: -1.76 (0.22), residues: 1510 helix: 0.56 (0.42), residues: 170 sheet: -0.71 (0.22), residues: 616 loop : -2.00 (0.22), residues: 724 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.446 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 124 average time/residue: 0.2162 time to fit residues: 40.9408 Evaluate side-chains 118 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1237 time to fit residues: 2.5628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 0.0010 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1055 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 11294 Z= 0.341 Angle : 0.601 8.473 15403 Z= 0.305 Chirality : 0.046 0.182 1782 Planarity : 0.004 0.043 2020 Dihedral : 6.008 129.157 1624 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.82 % Favored : 92.78 % Rotamer Outliers : 0.29 % 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: -1.90 (0.22), residues: 1510 helix: 0.23 (0.40), residues: 170 sheet: -0.79 (0.22), residues: 622 loop : -2.05 (0.22), residues: 718 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.288 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 119 average time/residue: 0.2209 time to fit residues: 39.3558 Evaluate side-chains 118 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0999 time to fit residues: 1.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 99 optimal weight: 0.1980 chunk 150 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11294 Z= 0.156 Angle : 0.504 6.400 15403 Z= 0.260 Chirality : 0.044 0.142 1782 Planarity : 0.003 0.043 2020 Dihedral : 5.588 124.329 1624 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.89 % Favored : 93.77 % Rotamer Outliers : 0.29 % 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 (0.22), residues: 1510 helix: 0.49 (0.41), residues: 176 sheet: -0.66 (0.22), residues: 617 loop : -1.99 (0.22), residues: 717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.383 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.2178 time to fit residues: 41.3778 Evaluate side-chains 124 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1063 time to fit residues: 2.2459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.0470 chunk 110 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.171466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128818 restraints weight = 13067.345| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.06 r_work: 0.3442 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work: 0.3390 rms_B_bonded: 2.78 restraints_weight: 0.1250 r_work: 0.3360 rms_B_bonded: 2.96 restraints_weight: 0.0625 r_work: 0.3325 rms_B_bonded: 3.26 restraints_weight: 0.0312 r_work: 0.3283 rms_B_bonded: 3.71 restraints_weight: 0.0156 r_work: 0.3232 rms_B_bonded: 4.35 restraints_weight: 0.0078 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11294 Z= 0.198 Angle : 0.527 8.239 15403 Z= 0.268 Chirality : 0.044 0.148 1782 Planarity : 0.003 0.042 2020 Dihedral : 5.601 124.399 1624 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.09 % Favored : 93.58 % Rotamer Outliers : 0.29 % 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 (0.22), residues: 1510 helix: 0.57 (0.41), residues: 174 sheet: -0.68 (0.22), residues: 621 loop : -2.01 (0.22), residues: 715 =============================================================================== Job complete usr+sys time: 2087.61 seconds wall clock time: 38 minutes 46.68 seconds (2326.68 seconds total)