Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 23:27:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmo_7964/04_2023/6dmo_7964.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmo_7964/04_2023/6dmo_7964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmo_7964/04_2023/6dmo_7964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmo_7964/04_2023/6dmo_7964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmo_7964/04_2023/6dmo_7964.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmo_7964/04_2023/6dmo_7964.pdb" } resolution = 4.1 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= 0.000 sd= 0.006 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 764 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5117 2.51 5 N 1284 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 906": "NH1" <-> "NH2" Residue "A ARG 942": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 982": "NH1" <-> "NH2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "A PHE 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7853 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7755 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 939} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.33, per 1000 atoms: 0.68 Number of scatterers: 7853 At special positions: 0 Unit cell: (90.553, 78.552, 142.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1410 8.00 N 1284 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B 1 " - " ASN A1000 " Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.2 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 60.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 removed outlier: 3.595A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.785A pdb=" N PHE A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 216 through 223 removed outlier: 3.598A pdb=" N ILE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.879A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 3.734A pdb=" N ALA A 239 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.867A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.840A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 389 through 411 removed outlier: 4.270A pdb=" N VAL A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.280A pdb=" N ASP A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 435 No H-bonds generated for 'chain 'A' and resid 434 through 435' Processing helix chain 'A' and resid 436 through 437 No H-bonds generated for 'chain 'A' and resid 436 through 437' Processing helix chain 'A' and resid 438 through 457 Processing helix chain 'A' and resid 466 through 491 removed outlier: 4.131A pdb=" N GLY A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 526 removed outlier: 3.622A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 563 removed outlier: 3.929A pdb=" N THR A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 604 Proline residue: A 593 - end of helix Processing helix chain 'A' and resid 732 through 744 Proline residue: A 742 - end of helix Processing helix chain 'A' and resid 750 through 770 removed outlier: 3.890A pdb=" N ILE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 815 through 829 removed outlier: 4.100A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 863 removed outlier: 4.311A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 885 removed outlier: 3.630A pdb=" N VAL A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 919 through 930 Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.860A pdb=" N TYR A 934 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1003 removed outlier: 3.612A pdb=" N PHE A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 Processing helix chain 'A' and resid 1026 through 1046 Processing helix chain 'A' and resid 1052 through 1075 removed outlier: 4.015A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1106 removed outlier: 5.137A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1138 removed outlier: 3.716A pdb=" N ALA A1118 " --> pdb=" O ARG A1114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Proline residue: A1125 - end of helix Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1146 through 1178 removed outlier: 5.043A pdb=" N ALA A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 366 removed outlier: 3.931A pdb=" N LEU A 360 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 158 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 156 " --> pdb=" O PHE A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 removed outlier: 7.165A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.618A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 801 " --> pdb=" O LEU A 978 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2410 1.34 - 1.46: 1907 1.46 - 1.58: 3658 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 8044 Sorted by residual: bond pdb=" C MET A 869 " pdb=" N PRO A 870 " ideal model delta sigma weight residual 1.336 1.370 -0.034 9.80e-03 1.04e+04 1.23e+01 bond pdb=" C1 NAG A1804 " pdb=" O5 NAG A1804 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C PRO A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.83e+00 bond pdb=" C1 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" CB PRO A1082 " pdb=" CG PRO A1082 " ideal model delta sigma weight residual 1.492 1.382 0.110 5.00e-02 4.00e+02 4.86e+00 ... (remaining 8039 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.27: 129 104.27 - 111.75: 3593 111.75 - 119.23: 2994 119.23 - 126.71: 4089 126.71 - 134.20: 132 Bond angle restraints: 10937 Sorted by residual: angle pdb=" N TYR A 224 " pdb=" CA TYR A 224 " pdb=" C TYR A 224 " ideal model delta sigma weight residual 109.48 96.78 12.70 1.75e+00 3.27e-01 5.26e+01 angle pdb=" N GLU A 534 " pdb=" CA GLU A 534 " pdb=" C GLU A 534 " ideal model delta sigma weight residual 112.72 106.95 5.77 1.28e+00 6.10e-01 2.04e+01 angle pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta sigma weight residual 121.80 132.76 -10.96 2.44e+00 1.68e-01 2.02e+01 angle pdb=" N ILE A 219 " pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 111.05 116.54 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" CG1 ILE A 815 " pdb=" CB ILE A 815 " pdb=" CG2 ILE A 815 " ideal model delta sigma weight residual 110.70 97.79 12.91 3.00e+00 1.11e-01 1.85e+01 ... (remaining 10932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4290 17.81 - 35.62: 313 35.62 - 53.43: 72 53.43 - 71.23: 7 71.23 - 89.04: 11 Dihedral angle restraints: 4693 sinusoidal: 1827 harmonic: 2866 Sorted by residual: dihedral pdb=" CA ASN A1049 " pdb=" C ASN A1049 " pdb=" N PRO A1050 " pdb=" CA PRO A1050 " ideal model delta harmonic sigma weight residual 180.00 -124.52 -55.48 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 -177.96 -89.04 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA LYS A 867 " pdb=" C LYS A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual -180.00 -131.82 -48.18 0 5.00e+00 4.00e-02 9.28e+01 ... (remaining 4690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 960 0.067 - 0.135: 255 0.135 - 0.202: 43 0.202 - 0.270: 6 0.270 - 0.337: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE A 815 " pdb=" CA ILE A 815 " pdb=" CG1 ILE A 815 " pdb=" CG2 ILE A 815 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.79e+00 ... (remaining 1263 not shown) Planarity restraints: 1370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1049 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO A1050 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1050 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1050 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 741 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 742 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 742 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 742 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1165 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C LEU A1165 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A1165 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A1166 " -0.015 2.00e-02 2.50e+03 ... (remaining 1367 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 21 2.39 - 3.02: 4207 3.02 - 3.65: 12274 3.65 - 4.27: 16593 4.27 - 4.90: 26909 Nonbonded interactions: 60004 Sorted by model distance: nonbonded pdb=" O ASN A 120 " pdb=" OG SER A 494 " model vdw 1.764 2.440 nonbonded pdb=" O GLU A 864 " pdb=" CG2 THR A 865 " model vdw 2.038 3.460 nonbonded pdb=" O ALA A 939 " pdb=" CD1 ILE A 941 " model vdw 2.276 3.460 nonbonded pdb=" OE1 GLN A 400 " pdb=" OG1 THR A 425 " model vdw 2.280 2.440 nonbonded pdb=" O ASN A 154 " pdb=" NE2 GLN A 156 " model vdw 2.285 2.520 ... (remaining 59999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 3.280 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.620 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.008 0.110 8044 Z= 0.502 Angle : 1.271 12.908 10937 Z= 0.656 Chirality : 0.063 0.337 1266 Planarity : 0.009 0.078 1364 Dihedral : 13.730 82.995 2840 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.07 % Favored : 88.63 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.21 % 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: -4.11 (0.21), residues: 976 helix: -2.12 (0.17), residues: 553 sheet: -2.15 (0.71), residues: 47 loop : -3.63 (0.27), residues: 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 303 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 4 residues processed: 316 average time/residue: 0.2144 time to fit residues: 89.9699 Evaluate side-chains 198 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0806 time to fit residues: 1.8184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.0000 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 358 HIS A 584 ASN A 802 ASN A 853 GLN A 929 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8044 Z= 0.226 Angle : 0.871 18.834 10937 Z= 0.425 Chirality : 0.051 0.579 1266 Planarity : 0.006 0.072 1364 Dihedral : 7.154 51.297 1061 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.45 % Favored : 89.45 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.11 % 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: -2.15 (0.26), residues: 976 helix: -0.22 (0.21), residues: 548 sheet: -1.80 (0.78), residues: 51 loop : -3.24 (0.29), residues: 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.2026 time to fit residues: 65.3725 Evaluate side-chains 164 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 160 GLN A 282 GLN A 289 HIS A 358 HIS ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN A 915 ASN A 950 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8044 Z= 0.219 Angle : 0.789 9.150 10937 Z= 0.391 Chirality : 0.046 0.289 1266 Planarity : 0.006 0.066 1364 Dihedral : 6.511 49.415 1061 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.48 % Favored : 88.42 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.21 % 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: -1.35 (0.27), residues: 976 helix: 0.51 (0.22), residues: 546 sheet: -1.73 (0.76), residues: 51 loop : -2.98 (0.31), residues: 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.2432 time to fit residues: 71.1361 Evaluate side-chains 155 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 365 GLN A 466 GLN A 802 ASN A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8044 Z= 0.201 Angle : 0.769 13.187 10937 Z= 0.376 Chirality : 0.046 0.291 1266 Planarity : 0.005 0.070 1364 Dihedral : 6.134 48.206 1061 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.76 % Favored : 89.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % 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: -1.00 (0.28), residues: 976 helix: 0.87 (0.22), residues: 541 sheet: -1.81 (0.75), residues: 51 loop : -2.85 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1912 time to fit residues: 51.9531 Evaluate side-chains 138 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 358 HIS A 828 ASN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 8044 Z= 0.215 Angle : 0.753 9.870 10937 Z= 0.368 Chirality : 0.045 0.257 1266 Planarity : 0.005 0.071 1364 Dihedral : 5.902 46.491 1061 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.55 % Favored : 89.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 976 helix: 1.02 (0.22), residues: 545 sheet: -1.53 (0.77), residues: 51 loop : -2.78 (0.32), residues: 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1804 time to fit residues: 46.7818 Evaluate side-chains 142 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 358 HIS A 802 ASN A 871 ASN A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8044 Z= 0.208 Angle : 0.752 11.758 10937 Z= 0.366 Chirality : 0.045 0.258 1266 Planarity : 0.005 0.071 1364 Dihedral : 5.787 45.407 1061 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.28), residues: 976 helix: 1.23 (0.23), residues: 541 sheet: -1.53 (0.77), residues: 51 loop : -2.68 (0.32), residues: 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1900 time to fit residues: 50.5677 Evaluate side-chains 151 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 289 HIS A 358 HIS A 520 HIS A 828 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8044 Z= 0.192 Angle : 0.761 13.939 10937 Z= 0.367 Chirality : 0.046 0.250 1266 Planarity : 0.005 0.070 1364 Dihedral : 5.568 43.788 1061 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.28), residues: 976 helix: 1.24 (0.23), residues: 534 sheet: -1.84 (0.73), residues: 50 loop : -2.67 (0.31), residues: 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1852 time to fit residues: 49.8851 Evaluate side-chains 141 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.0070 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 289 HIS A 358 HIS A 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8044 Z= 0.191 Angle : 0.760 11.312 10937 Z= 0.363 Chirality : 0.045 0.256 1266 Planarity : 0.005 0.071 1364 Dihedral : 5.455 43.033 1061 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 976 helix: 1.29 (0.23), residues: 531 sheet: -1.64 (0.74), residues: 50 loop : -2.63 (0.32), residues: 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1777 time to fit residues: 47.1890 Evaluate side-chains 134 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.0770 chunk 57 optimal weight: 0.4980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 258 ASN A 289 HIS A 358 HIS ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8044 Z= 0.192 Angle : 0.774 11.906 10937 Z= 0.368 Chirality : 0.046 0.302 1266 Planarity : 0.005 0.068 1364 Dihedral : 5.403 41.258 1061 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.28), residues: 976 helix: 1.20 (0.22), residues: 534 sheet: -1.72 (0.73), residues: 50 loop : -2.63 (0.32), residues: 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1789 time to fit residues: 47.0421 Evaluate side-chains 145 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 289 HIS A 358 HIS A 520 HIS A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 8044 Z= 0.202 Angle : 0.772 12.142 10937 Z= 0.373 Chirality : 0.046 0.323 1266 Planarity : 0.005 0.068 1364 Dihedral : 5.357 40.327 1061 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 976 helix: 1.19 (0.22), residues: 533 sheet: -1.65 (0.74), residues: 50 loop : -2.54 (0.32), residues: 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1764 time to fit residues: 46.8500 Evaluate side-chains 134 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 289 HIS A 358 HIS A 375 HIS ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103751 restraints weight = 20443.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.106750 restraints weight = 12115.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108870 restraints weight = 8354.181| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.8463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 8044 Z= 0.212 Angle : 0.760 12.029 10937 Z= 0.367 Chirality : 0.045 0.229 1266 Planarity : 0.005 0.068 1364 Dihedral : 5.304 40.060 1061 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 976 helix: 1.25 (0.22), residues: 536 sheet: -1.67 (0.75), residues: 50 loop : -2.55 (0.32), residues: 390 =============================================================================== Job complete usr+sys time: 1891.36 seconds wall clock time: 34 minutes 54.03 seconds (2094.03 seconds total)