Starting phenix.real_space_refine on Mon Nov 17 21:02:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmo_7964/11_2025/6dmo_7964.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmo_7964/11_2025/6dmo_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dmo_7964/11_2025/6dmo_7964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmo_7964/11_2025/6dmo_7964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dmo_7964/11_2025/6dmo_7964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmo_7964/11_2025/6dmo_7964.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} 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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.82, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 0.58 Conformation dependent library (CDL) restraints added in 329.1 milliseconds 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: 0.26 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: 1.20 Time building geometry restraints manager: 0.79 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: 0.00 - 2.58: 10374 2.58 - 5.16: 455 5.16 - 7.74: 82 7.74 - 10.33: 19 10.33 - 12.91: 7 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: 4419 17.81 - 35.62: 323 35.62 - 53.43: 78 53.43 - 71.23: 9 71.23 - 89.04: 11 Dihedral angle restraints: 4840 sinusoidal: 1974 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 4837 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 3.040 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 3.040 nonbonded pdb=" O ASN A 154 " pdb=" NE2 GLN A 156 " model vdw 2.285 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.900 ------------------------------------------------------------------------------- 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 8054 Z= 0.355 Angle : 1.289 12.908 10964 Z= 0.659 Chirality : 0.063 0.337 1266 Planarity : 0.009 0.078 1364 Dihedral : 13.720 82.995 2987 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 % Allowed : 10.77 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 786 TYR 0.035 0.003 TYR A 812 PHE 0.037 0.004 PHE A1153 TRP 0.027 0.003 TRP A 399 HIS 0.020 0.003 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 8044) covalent geometry : angle 1.27061 (10937) SS BOND : bond 0.00994 ( 3) SS BOND : angle 2.12103 ( 6) hydrogen bonds : bond 0.14799 ( 419) hydrogen bonds : angle 7.11781 ( 1245) link_BETA1-4 : bond 0.00563 ( 1) link_BETA1-4 : angle 2.18731 ( 3) link_NAG-ASN : bond 0.00602 ( 6) link_NAG-ASN : angle 5.30445 ( 18) *********************** 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 to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.274 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: A 74 LYS cc_start: 0.8126 (pttt) cc_final: 0.7919 (tptt) REVERT: A 86 LEU cc_start: 0.8533 (mt) cc_final: 0.8260 (tp) REVERT: A 94 ILE cc_start: 0.8773 (mt) cc_final: 0.8520 (tp) REVERT: A 172 THR cc_start: 0.7547 (p) cc_final: 0.7155 (p) REVERT: A 254 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6164 (tm) REVERT: A 319 MET cc_start: 0.7461 (mpm) cc_final: 0.7067 (mmm) REVERT: A 373 TYR cc_start: 0.8123 (t80) cc_final: 0.7567 (t80) REVERT: A 430 ILE cc_start: 0.8330 (mm) cc_final: 0.8114 (pt) REVERT: A 791 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 1087 ILE cc_start: 0.8253 (mm) cc_final: 0.8037 (mm) REVERT: A 1105 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7613 (tm) REVERT: A 1166 ASN cc_start: 0.8414 (t0) cc_final: 0.8052 (t0) REVERT: A 1178 PHE cc_start: 0.7848 (p90) cc_final: 0.7575 (t80) outliers start: 23 outliers final: 3 residues processed: 316 average time/residue: 0.0908 time to fit residues: 38.4802 Evaluate side-chains 200 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 289 HIS A 358 HIS A 400 GLN A 584 ASN A 802 ASN A 853 GLN A 929 ASN A 950 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110403 restraints weight = 20529.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113514 restraints weight = 12138.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115639 restraints weight = 8341.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117246 restraints weight = 6373.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118241 restraints weight = 5205.198| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8054 Z= 0.169 Angle : 0.900 11.540 10964 Z= 0.439 Chirality : 0.053 0.715 1266 Planarity : 0.006 0.063 1364 Dihedral : 7.928 54.263 1208 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.24 % Allowed : 4.84 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.26), residues: 976 helix: -0.25 (0.21), residues: 546 sheet: -1.86 (0.76), residues: 52 loop : -3.23 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 536 TYR 0.020 0.002 TYR A 142 PHE 0.033 0.002 PHE A 790 TRP 0.023 0.002 TRP A 399 HIS 0.006 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8044) covalent geometry : angle 0.87244 (10937) SS BOND : bond 0.00630 ( 3) SS BOND : angle 2.13061 ( 6) hydrogen bonds : bond 0.05020 ( 419) hydrogen bonds : angle 5.40451 ( 1245) link_BETA1-4 : bond 0.00157 ( 1) link_BETA1-4 : angle 0.76526 ( 3) link_NAG-ASN : bond 0.00537 ( 6) link_NAG-ASN : angle 5.41131 ( 18) *********************** 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 229 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.301 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: A 74 LYS cc_start: 0.8436 (pttt) cc_final: 0.8074 (tptt) REVERT: A 128 LEU cc_start: 0.7026 (pt) cc_final: 0.6717 (pp) REVERT: A 373 TYR cc_start: 0.8018 (t80) cc_final: 0.7389 (t80) REVERT: A 476 LEU cc_start: 0.9317 (tt) cc_final: 0.8920 (pp) REVERT: A 791 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8560 (mt) REVERT: A 1015 PHE cc_start: 0.6831 (m-80) cc_final: 0.6619 (m-10) REVERT: A 1087 ILE cc_start: 0.8195 (mm) cc_final: 0.7917 (mm) REVERT: A 1117 LEU cc_start: 0.8689 (mp) cc_final: 0.8376 (mt) REVERT: A 1166 ASN cc_start: 0.8658 (t0) cc_final: 0.8363 (t0) REVERT: A 1178 PHE cc_start: 0.7872 (p90) cc_final: 0.7490 (t80) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.0767 time to fit residues: 24.6743 Evaluate side-chains 168 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 282 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 365 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN A 915 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.123537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103987 restraints weight = 20694.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106909 restraints weight = 12522.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108979 restraints weight = 8736.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110435 restraints weight = 6714.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111458 restraints weight = 5520.016| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8054 Z= 0.180 Angle : 0.859 12.555 10964 Z= 0.421 Chirality : 0.048 0.297 1266 Planarity : 0.006 0.066 1364 Dihedral : 7.535 59.821 1208 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 0.36 % Allowed : 6.30 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.27), residues: 976 helix: 0.44 (0.22), residues: 543 sheet: -1.73 (0.78), residues: 52 loop : -2.97 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 401 TYR 0.020 0.002 TYR A 922 PHE 0.031 0.002 PHE A 790 TRP 0.030 0.002 TRP A 926 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8044) covalent geometry : angle 0.83448 (10937) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.77133 ( 6) hydrogen bonds : bond 0.04718 ( 419) hydrogen bonds : angle 5.08122 ( 1245) link_BETA1-4 : bond 0.00031 ( 1) link_BETA1-4 : angle 0.76915 ( 3) link_NAG-ASN : bond 0.00999 ( 6) link_NAG-ASN : angle 5.04142 ( 18) *********************** 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 221 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8484 (pttt) cc_final: 0.8104 (tptt) REVERT: A 103 VAL cc_start: 0.7720 (t) cc_final: 0.7394 (p) REVERT: A 200 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 228 ILE cc_start: 0.8724 (mt) cc_final: 0.8431 (pt) REVERT: A 419 VAL cc_start: 0.8380 (m) cc_final: 0.8129 (m) REVERT: A 432 LYS cc_start: 0.8214 (tppt) cc_final: 0.7847 (tppt) REVERT: A 791 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 833 MET cc_start: 0.6286 (tpp) cc_final: 0.5955 (tpp) REVERT: A 1056 ILE cc_start: 0.8537 (mm) cc_final: 0.8173 (mm) REVERT: A 1066 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7379 (tm-30) REVERT: A 1068 PHE cc_start: 0.7725 (t80) cc_final: 0.7460 (t80) REVERT: A 1087 ILE cc_start: 0.8408 (mm) cc_final: 0.8111 (mm) REVERT: A 1097 THR cc_start: 0.8562 (p) cc_final: 0.8267 (p) REVERT: A 1162 LEU cc_start: 0.8281 (tp) cc_final: 0.8035 (tp) outliers start: 3 outliers final: 0 residues processed: 220 average time/residue: 0.0803 time to fit residues: 24.5438 Evaluate side-chains 161 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.124383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104897 restraints weight = 20766.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107893 restraints weight = 12237.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110044 restraints weight = 8408.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111561 restraints weight = 6406.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.112632 restraints weight = 5254.380| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8054 Z= 0.141 Angle : 0.819 11.830 10964 Z= 0.393 Chirality : 0.047 0.268 1266 Planarity : 0.005 0.070 1364 Dihedral : 6.580 53.122 1208 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.27), residues: 976 helix: 0.67 (0.22), residues: 539 sheet: -1.48 (0.76), residues: 51 loop : -2.95 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 772 TYR 0.015 0.001 TYR A 222 PHE 0.023 0.002 PHE A 790 TRP 0.034 0.002 TRP A 399 HIS 0.007 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8044) covalent geometry : angle 0.79734 (10937) SS BOND : bond 0.00157 ( 3) SS BOND : angle 1.69926 ( 6) hydrogen bonds : bond 0.04323 ( 419) hydrogen bonds : angle 4.91541 ( 1245) link_BETA1-4 : bond 0.00387 ( 1) link_BETA1-4 : angle 0.72657 ( 3) link_NAG-ASN : bond 0.00843 ( 6) link_NAG-ASN : angle 4.65729 ( 18) *********************** 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 201 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8364 (pttt) cc_final: 0.8029 (tptt) REVERT: A 103 VAL cc_start: 0.7697 (t) cc_final: 0.7385 (p) REVERT: A 292 MET cc_start: 0.4893 (mmp) cc_final: 0.3748 (mmp) REVERT: A 432 LYS cc_start: 0.8396 (tppt) cc_final: 0.7984 (tppt) REVERT: A 475 LEU cc_start: 0.8425 (pp) cc_final: 0.8216 (tt) REVERT: A 522 PHE cc_start: 0.8314 (t80) cc_final: 0.8075 (t80) REVERT: A 791 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8727 (mp) REVERT: A 833 MET cc_start: 0.6239 (tpp) cc_final: 0.5989 (tpp) REVERT: A 1087 ILE cc_start: 0.8264 (mm) cc_final: 0.8040 (mm) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0771 time to fit residues: 22.0655 Evaluate side-chains 151 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 258 ASN A 828 ASN A 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.119731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100659 restraints weight = 20930.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.103568 restraints weight = 12308.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105624 restraints weight = 8466.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107113 restraints weight = 6459.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107734 restraints weight = 5292.093| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8054 Z= 0.163 Angle : 0.803 12.290 10964 Z= 0.397 Chirality : 0.047 0.237 1266 Planarity : 0.005 0.070 1364 Dihedral : 6.271 45.412 1208 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.27), residues: 976 helix: 0.86 (0.22), residues: 545 sheet: -1.35 (0.78), residues: 49 loop : -2.82 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 772 TYR 0.026 0.002 TYR A 934 PHE 0.026 0.002 PHE A 826 TRP 0.042 0.003 TRP A 278 HIS 0.008 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8044) covalent geometry : angle 0.78284 (10937) SS BOND : bond 0.00473 ( 3) SS BOND : angle 1.18484 ( 6) hydrogen bonds : bond 0.04424 ( 419) hydrogen bonds : angle 4.93865 ( 1245) link_BETA1-4 : bond 0.00021 ( 1) link_BETA1-4 : angle 1.00605 ( 3) link_NAG-ASN : bond 0.00670 ( 6) link_NAG-ASN : angle 4.48117 ( 18) *********************** 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 197 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8361 (pttt) cc_final: 0.8130 (tptt) REVERT: A 103 VAL cc_start: 0.7680 (t) cc_final: 0.7425 (p) REVERT: A 432 LYS cc_start: 0.8300 (tppt) cc_final: 0.7934 (tppt) REVERT: A 475 LEU cc_start: 0.8549 (pp) cc_final: 0.8306 (tt) REVERT: A 791 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9068 (mp) REVERT: A 1146 ASP cc_start: 0.7160 (t0) cc_final: 0.6886 (t0) REVERT: A 1162 LEU cc_start: 0.8585 (tp) cc_final: 0.8202 (tp) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.0734 time to fit residues: 20.8174 Evaluate side-chains 147 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 828 ASN A 871 ASN A 950 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093608 restraints weight = 21013.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096455 restraints weight = 11979.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098471 restraints weight = 8143.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099990 restraints weight = 6191.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.100892 restraints weight = 5058.467| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.7692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8054 Z= 0.207 Angle : 0.858 11.616 10964 Z= 0.423 Chirality : 0.050 0.287 1266 Planarity : 0.006 0.073 1364 Dihedral : 6.419 45.376 1208 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.27), residues: 976 helix: 0.66 (0.22), residues: 548 sheet: -1.54 (0.75), residues: 51 loop : -2.75 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 962 TYR 0.019 0.002 TYR A 934 PHE 0.024 0.002 PHE A1068 TRP 0.027 0.002 TRP A 129 HIS 0.005 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8044) covalent geometry : angle 0.84148 (10937) SS BOND : bond 0.00411 ( 3) SS BOND : angle 1.47281 ( 6) hydrogen bonds : bond 0.04569 ( 419) hydrogen bonds : angle 4.98589 ( 1245) link_BETA1-4 : bond 0.00688 ( 1) link_BETA1-4 : angle 0.82423 ( 3) link_NAG-ASN : bond 0.00759 ( 6) link_NAG-ASN : angle 4.22339 ( 18) *********************** 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 195 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9040 (tt) cc_final: 0.8417 (tt) REVERT: A 83 PHE cc_start: 0.8153 (m-10) cc_final: 0.7864 (m-80) REVERT: A 108 ILE cc_start: 0.8156 (pt) cc_final: 0.7930 (tt) REVERT: A 281 MET cc_start: 0.8170 (mtp) cc_final: 0.7927 (mtp) REVERT: A 372 MET cc_start: 0.7749 (ttm) cc_final: 0.7516 (ttm) REVERT: A 475 LEU cc_start: 0.8609 (pp) cc_final: 0.8404 (tt) REVERT: A 993 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8624 (mmtm) REVERT: A 1056 ILE cc_start: 0.8998 (mm) cc_final: 0.8784 (mm) REVERT: A 1097 THR cc_start: 0.9020 (p) cc_final: 0.8786 (p) REVERT: A 1146 ASP cc_start: 0.7478 (t0) cc_final: 0.7239 (t0) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.0744 time to fit residues: 20.6975 Evaluate side-chains 150 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.116061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097294 restraints weight = 20871.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.100119 restraints weight = 12211.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102196 restraints weight = 8412.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103586 restraints weight = 6399.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104378 restraints weight = 5264.951| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.8179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8054 Z= 0.146 Angle : 0.795 11.720 10964 Z= 0.387 Chirality : 0.047 0.247 1266 Planarity : 0.005 0.074 1364 Dihedral : 6.196 44.562 1208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.28), residues: 976 helix: 0.92 (0.22), residues: 540 sheet: -1.40 (0.80), residues: 51 loop : -2.70 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 960 TYR 0.019 0.001 TYR A 934 PHE 0.026 0.002 PHE A1031 TRP 0.022 0.002 TRP A 129 HIS 0.007 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8044) covalent geometry : angle 0.77735 (10937) SS BOND : bond 0.00220 ( 3) SS BOND : angle 1.89609 ( 6) hydrogen bonds : bond 0.04164 ( 419) hydrogen bonds : angle 4.82236 ( 1245) link_BETA1-4 : bond 0.00151 ( 1) link_BETA1-4 : angle 1.00411 ( 3) link_NAG-ASN : bond 0.00753 ( 6) link_NAG-ASN : angle 4.09613 ( 18) *********************** 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 200 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8915 (tt) cc_final: 0.8187 (tt) REVERT: A 83 PHE cc_start: 0.7854 (m-10) cc_final: 0.7480 (m-80) REVERT: A 108 ILE cc_start: 0.8198 (pt) cc_final: 0.7970 (tt) REVERT: A 825 SER cc_start: 0.9035 (m) cc_final: 0.8790 (p) REVERT: A 1146 ASP cc_start: 0.7257 (t0) cc_final: 0.7016 (t0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0812 time to fit residues: 22.8293 Evaluate side-chains 140 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 84 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 520 HIS ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.099403 restraints weight = 21131.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102389 restraints weight = 12062.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104468 restraints weight = 8114.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.105794 restraints weight = 6105.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.106888 restraints weight = 5010.729| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.8521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8054 Z= 0.140 Angle : 0.816 15.811 10964 Z= 0.391 Chirality : 0.047 0.241 1266 Planarity : 0.005 0.072 1364 Dihedral : 6.175 44.652 1208 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.12 % Allowed : 2.06 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.27), residues: 976 helix: 0.91 (0.22), residues: 541 sheet: -1.31 (0.78), residues: 51 loop : -2.59 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 770 TYR 0.021 0.001 TYR A1009 PHE 0.056 0.002 PHE A1031 TRP 0.019 0.001 TRP A 129 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8044) covalent geometry : angle 0.79303 (10937) SS BOND : bond 0.00146 ( 3) SS BOND : angle 1.61353 ( 6) hydrogen bonds : bond 0.03991 ( 419) hydrogen bonds : angle 4.68118 ( 1245) link_BETA1-4 : bond 0.00103 ( 1) link_BETA1-4 : angle 0.94612 ( 3) link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 4.68834 ( 18) *********************** 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 185 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 LEU cc_start: 0.9087 (tt) cc_final: 0.8854 (pp) REVERT: A 561 MET cc_start: 0.8002 (tpt) cc_final: 0.7702 (tpt) REVERT: A 825 SER cc_start: 0.8986 (m) cc_final: 0.8783 (p) REVERT: A 1146 ASP cc_start: 0.7198 (t0) cc_final: 0.6933 (t0) REVERT: A 1162 LEU cc_start: 0.8386 (tp) cc_final: 0.8145 (tp) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.0714 time to fit residues: 19.1594 Evaluate side-chains 142 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.114475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095604 restraints weight = 21505.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098479 restraints weight = 12491.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.100500 restraints weight = 8537.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101930 restraints weight = 6502.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.102668 restraints weight = 5327.895| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.9015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8054 Z= 0.171 Angle : 0.838 13.863 10964 Z= 0.408 Chirality : 0.048 0.245 1266 Planarity : 0.005 0.074 1364 Dihedral : 5.916 43.050 1208 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.27), residues: 976 helix: 0.84 (0.22), residues: 542 sheet: -1.33 (0.79), residues: 51 loop : -2.59 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 960 TYR 0.021 0.002 TYR A1009 PHE 0.033 0.002 PHE A1031 TRP 0.021 0.002 TRP A 129 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8044) covalent geometry : angle 0.81877 (10937) SS BOND : bond 0.00169 ( 3) SS BOND : angle 2.34892 ( 6) hydrogen bonds : bond 0.04378 ( 419) hydrogen bonds : angle 4.78296 ( 1245) link_BETA1-4 : bond 0.00038 ( 1) link_BETA1-4 : angle 1.17776 ( 3) link_NAG-ASN : bond 0.00316 ( 6) link_NAG-ASN : angle 4.26359 ( 18) *********************** 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 183 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9003 (tt) cc_final: 0.8656 (tt) REVERT: A 177 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 220 ILE cc_start: 0.6234 (mm) cc_final: 0.5551 (mm) REVERT: A 825 SER cc_start: 0.9111 (m) cc_final: 0.8871 (p) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0726 time to fit residues: 19.2884 Evaluate side-chains 136 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 584 ASN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.118039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099144 restraints weight = 21249.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102048 restraints weight = 12327.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.104164 restraints weight = 8440.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.105514 restraints weight = 6392.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106609 restraints weight = 5278.190| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.9236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8054 Z= 0.145 Angle : 0.820 12.200 10964 Z= 0.395 Chirality : 0.048 0.320 1266 Planarity : 0.005 0.075 1364 Dihedral : 5.718 42.869 1208 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.28), residues: 976 helix: 0.94 (0.22), residues: 524 sheet: -1.24 (0.80), residues: 50 loop : -2.50 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 536 TYR 0.017 0.001 TYR A1009 PHE 0.019 0.002 PHE A1031 TRP 0.047 0.002 TRP A 278 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8044) covalent geometry : angle 0.80496 (10937) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.86701 ( 6) hydrogen bonds : bond 0.04137 ( 419) hydrogen bonds : angle 4.70500 ( 1245) link_BETA1-4 : bond 0.00330 ( 1) link_BETA1-4 : angle 1.02110 ( 3) link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 3.80163 ( 18) ********************** 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 180 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.9277 (mt) cc_final: 0.8967 (tp) REVERT: A 154 ASN cc_start: 0.9067 (t0) cc_final: 0.8345 (m110) REVERT: A 216 MET cc_start: 0.3125 (tpt) cc_final: 0.2571 (tpp) REVERT: A 366 LEU cc_start: 0.9193 (mt) cc_final: 0.8815 (mt) REVERT: A 1018 TRP cc_start: 0.6325 (t-100) cc_final: 0.5879 (t-100) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0695 time to fit residues: 18.3418 Evaluate side-chains 138 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 0.0030 chunk 91 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 846 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.118289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099490 restraints weight = 21187.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102443 restraints weight = 12458.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104531 restraints weight = 8523.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105841 restraints weight = 6481.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106950 restraints weight = 5355.997| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.9488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8054 Z= 0.141 Angle : 0.804 12.359 10964 Z= 0.388 Chirality : 0.047 0.291 1266 Planarity : 0.005 0.075 1364 Dihedral : 5.613 42.293 1208 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.12 % Allowed : 0.61 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 976 helix: 0.90 (0.22), residues: 527 sheet: -1.18 (0.77), residues: 50 loop : -2.52 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 536 TYR 0.018 0.002 TYR A1009 PHE 0.017 0.002 PHE A 790 TRP 0.047 0.002 TRP A 278 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8044) covalent geometry : angle 0.79046 (10937) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.85243 ( 6) hydrogen bonds : bond 0.03939 ( 419) hydrogen bonds : angle 4.63586 ( 1245) link_BETA1-4 : bond 0.00212 ( 1) link_BETA1-4 : angle 1.05112 ( 3) link_NAG-ASN : bond 0.00329 ( 6) link_NAG-ASN : angle 3.52265 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.96 seconds wall clock time: 25 minutes 0.48 seconds (1500.48 seconds total)