Starting phenix.real_space_refine on Tue Mar 3 17:16:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oeu_7795/03_2026/6oeu_7795.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeu_7795/03_2026/6oeu_7795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oeu_7795/03_2026/6oeu_7795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeu_7795/03_2026/6oeu_7795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oeu_7795/03_2026/6oeu_7795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeu_7795/03_2026/6oeu_7795.map" } resolution = 3.5 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= 0.003 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4734 2.51 5 N 1215 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7310 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7198 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 39, 'TRANS': 924} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'TYR:plan': 11, 'ASN:plan1': 8, 'ARG:plan': 5, 'GLN:plan1': 5, 'TRP:plan': 5, 'GLU:plan': 8, 'ASP:plan': 9, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 267 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: "C" 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: "D" 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: "E" 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 Time building chain proxies: 1.70, per 1000 atoms: 0.23 Number of scatterers: 7310 At special positions: 0 Unit cell: (133, 83, 87, 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 34 16.00 O 1327 8.00 N 1215 7.00 C 4734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG E 1 " - " ASN A1000 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 283.4 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 59.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 77 through 94 removed outlier: 4.616A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.692A pdb=" N GLY A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 removed outlier: 4.015A pdb=" N ARG A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.991A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.676A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.834A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 342' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.606A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.603A pdb=" N VAL A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 502 through 525 removed outlier: 4.478A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 561 removed outlier: 5.271A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 602 Proline residue: A 593 - end of helix removed outlier: 3.559A pdb=" N ARG A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 746 through 770 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.660A pdb=" N ASP A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.843A pdb=" N ASP A 789 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.980A pdb=" N ASN A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 838 " --> pdb=" O GLU A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.627A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.674A pdb=" N SER A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 removed outlier: 3.595A pdb=" N TYR A 934 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1004 removed outlier: 3.689A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 3.549A pdb=" N TRP A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1048 removed outlier: 3.537A pdb=" N TRP A1027 " --> pdb=" O GLY A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1075 Processing helix chain 'A' and resid 1079 through 1102 removed outlier: 4.105A pdb=" N VAL A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A1091 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 removed outlier: 3.685A pdb=" N THR A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1106' Processing helix chain 'A' and resid 1112 through 1138 removed outlier: 3.574A pdb=" N VAL A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 5.199A 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 1142 Processing helix chain 'A' and resid 1147 through 1175 removed outlier: 5.149A pdb=" N LEU A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.674A pdb=" N ASN A 154 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 366 " --> pdb=" O ASN A 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 800 through 801 Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 975 407 hydrogen bonds defined for protein. 1191 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: 1.15 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1341 1.33 - 1.45: 1835 1.45 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7466 Sorted by residual: bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.456 1.504 -0.048 9.50e-03 1.11e+04 2.51e+01 bond pdb=" N VAL A 275 " pdb=" CA VAL A 275 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.04e-02 9.25e+03 2.05e+01 bond pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta sigma weight residual 1.455 1.484 -0.029 7.00e-03 2.04e+04 1.69e+01 bond pdb=" N ILE A 963 " pdb=" CA ILE A 963 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" N GLY A 214 " pdb=" CA GLY A 214 " ideal model delta sigma weight residual 1.446 1.486 -0.040 1.06e-02 8.90e+03 1.39e+01 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 9789 3.82 - 7.64: 372 7.64 - 11.45: 8 11.45 - 15.27: 1 15.27 - 19.09: 2 Bond angle restraints: 10172 Sorted by residual: angle pdb=" N SER A 415 " pdb=" CA SER A 415 " pdb=" C SER A 415 " ideal model delta sigma weight residual 110.23 91.14 19.09 1.45e+00 4.76e-01 1.73e+02 angle pdb=" N LEU A 121 " pdb=" CA LEU A 121 " pdb=" C LEU A 121 " ideal model delta sigma weight residual 108.69 93.01 15.68 1.77e+00 3.19e-01 7.85e+01 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 112.45 101.16 11.29 1.39e+00 5.18e-01 6.60e+01 angle pdb=" C SER A 415 " pdb=" CA SER A 415 " pdb=" CB SER A 415 " ideal model delta sigma weight residual 109.72 122.46 -12.74 1.66e+00 3.63e-01 5.89e+01 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" CB PRO A 252 " ideal model delta sigma weight residual 103.08 110.31 -7.23 9.70e-01 1.06e+00 5.56e+01 ... (remaining 10167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 4135 21.47 - 42.93: 302 42.93 - 64.40: 41 64.40 - 85.86: 11 85.86 - 107.33: 4 Dihedral angle restraints: 4493 sinusoidal: 1693 harmonic: 2800 Sorted by residual: dihedral pdb=" CA SER A 313 " pdb=" C SER A 313 " pdb=" N THR A 314 " pdb=" CA THR A 314 " ideal model delta harmonic sigma weight residual -180.00 -144.14 -35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" C ALA A 246 " pdb=" N ALA A 246 " pdb=" CA ALA A 246 " pdb=" CB ALA A 246 " ideal model delta harmonic sigma weight residual -122.60 -106.73 -15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" CA HIS A 201 " pdb=" C HIS A 201 " pdb=" N LEU A 202 " pdb=" CA LEU A 202 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 1214 0.333 - 0.666: 2 0.666 - 0.999: 1 0.999 - 1.332: 0 1.332 - 1.665: 3 Chirality restraints: 1220 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-02 2.50e+03 6.93e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.18e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-02 2.50e+03 4.53e+03 ... (remaining 1217 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1000 " -0.263 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" CG ASN A1000 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A1000 " 0.080 2.00e-02 2.50e+03 pdb=" ND2 ASN A1000 " 0.389 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 229 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ILE A 229 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE A 229 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 230 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 156 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLN A 156 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 156 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 157 " 0.018 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 168 2.71 - 3.25: 7011 3.25 - 3.80: 11318 3.80 - 4.35: 14002 4.35 - 4.90: 23666 Nonbonded interactions: 56165 Sorted by model distance: nonbonded pdb=" ND2 ASN A 141 " pdb=" C1 NAG B 1 " model vdw 2.157 3.550 nonbonded pdb=" ND2 ASN A 414 " pdb=" O5 NAG D 1 " model vdw 2.322 3.120 nonbonded pdb=" ND2 ASN A 414 " pdb=" C2 NAG D 1 " model vdw 2.396 3.550 nonbonded pdb=" O GLY A1129 " pdb=" OG SER A1132 " model vdw 2.397 3.040 nonbonded pdb=" O SER A 799 " pdb=" OG SER A 799 " model vdw 2.399 3.040 ... (remaining 56160 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 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 : 0.015 0.449 7471 Z= 1.129 Angle : 2.122 52.484 10187 Z= 1.431 Chirality : 0.112 1.665 1220 Planarity : 0.005 0.037 1278 Dihedral : 15.735 107.325 2685 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.33 % Favored : 89.56 % Rotamer: Outliers : 0.85 % Allowed : 12.36 % Favored : 86.79 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.81 (0.22), residues: 958 helix: -1.66 (0.18), residues: 542 sheet: -2.05 (0.71), residues: 43 loop : -3.88 (0.26), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 995 TYR 0.029 0.003 TYR A1001 PHE 0.035 0.003 PHE A 757 TRP 0.021 0.003 TRP A 337 HIS 0.009 0.002 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.01427 ( 7466) covalent geometry : angle 1.88166 (10172) hydrogen bonds : bond 0.14257 ( 407) hydrogen bonds : angle 7.80439 ( 1191) link_BETA1-4 : bond 0.07159 ( 4) link_BETA1-4 : angle 25.71556 ( 12) link_NAG-ASN : bond 0.44943 ( 1) link_NAG-ASN : angle 25.33300 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.7103 (t0) cc_final: 0.6897 (t0) REVERT: A 520 HIS cc_start: 0.7256 (t70) cc_final: 0.6121 (m-70) REVERT: A 979 ASN cc_start: 0.7621 (t0) cc_final: 0.6994 (t0) REVERT: A 1004 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7131 (tp) REVERT: A 1066 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6792 (mt-10) REVERT: A 1105 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6426 (pt) outliers start: 6 outliers final: 1 residues processed: 180 average time/residue: 0.0959 time to fit residues: 22.9401 Evaluate side-chains 119 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 124 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 312 ASN A 527 GLN A1166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.203820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177740 restraints weight = 10222.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.182509 restraints weight = 6055.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184894 restraints weight = 3699.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185607 restraints weight = 2792.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186130 restraints weight = 2665.051| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7471 Z= 0.146 Angle : 0.727 10.990 10187 Z= 0.361 Chirality : 0.044 0.374 1220 Planarity : 0.005 0.045 1278 Dihedral : 9.515 79.632 1198 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.70 % Allowed : 18.47 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.10 (0.26), residues: 958 helix: -0.27 (0.21), residues: 558 sheet: -1.57 (0.76), residues: 43 loop : -3.22 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 530 TYR 0.010 0.001 TYR A 452 PHE 0.031 0.002 PHE A 798 TRP 0.010 0.001 TRP A 926 HIS 0.005 0.001 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7466) covalent geometry : angle 0.71382 (10172) hydrogen bonds : bond 0.04584 ( 407) hydrogen bonds : angle 5.31058 ( 1191) link_BETA1-4 : bond 0.00784 ( 4) link_BETA1-4 : angle 2.46168 ( 12) link_NAG-ASN : bond 0.01168 ( 1) link_NAG-ASN : angle 6.51459 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3410 (tptt) cc_final: 0.2896 (mmtm) REVERT: A 154 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8647 (p0) REVERT: A 158 MET cc_start: 0.7944 (ttp) cc_final: 0.7570 (ttm) REVERT: A 602 ARG cc_start: 0.4891 (mmt180) cc_final: 0.3133 (ptp-170) REVERT: A 789 ASP cc_start: 0.6607 (m-30) cc_final: 0.6159 (m-30) outliers start: 19 outliers final: 8 residues processed: 145 average time/residue: 0.0684 time to fit residues: 14.3268 Evaluate side-chains 124 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 1117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 361 GLN A 375 HIS A 520 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.204329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.178221 restraints weight = 10353.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.182763 restraints weight = 6384.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.185303 restraints weight = 4000.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185979 restraints weight = 2964.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.186532 restraints weight = 2880.535| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7471 Z= 0.129 Angle : 0.653 9.620 10187 Z= 0.323 Chirality : 0.043 0.349 1220 Planarity : 0.005 0.051 1278 Dihedral : 7.877 57.796 1193 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.12 % Allowed : 21.73 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.45 (0.27), residues: 958 helix: 0.24 (0.22), residues: 568 sheet: -1.36 (0.81), residues: 37 loop : -2.99 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 80 TYR 0.021 0.001 TYR A 452 PHE 0.040 0.002 PHE A 798 TRP 0.011 0.001 TRP A 337 HIS 0.016 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7466) covalent geometry : angle 0.63803 (10172) hydrogen bonds : bond 0.03968 ( 407) hydrogen bonds : angle 4.98000 ( 1191) link_BETA1-4 : bond 0.00641 ( 4) link_BETA1-4 : angle 2.54629 ( 12) link_NAG-ASN : bond 0.01421 ( 1) link_NAG-ASN : angle 6.50775 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3379 (tptt) cc_final: 0.3102 (mmtm) REVERT: A 154 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (p0) REVERT: A 158 MET cc_start: 0.7886 (ttp) cc_final: 0.7450 (ttm) REVERT: A 372 MET cc_start: 0.8601 (tpp) cc_final: 0.8088 (ttm) REVERT: A 602 ARG cc_start: 0.4599 (mmt180) cc_final: 0.2941 (ptp-170) REVERT: A 789 ASP cc_start: 0.6793 (m-30) cc_final: 0.6468 (m-30) outliers start: 22 outliers final: 11 residues processed: 143 average time/residue: 0.0743 time to fit residues: 15.2386 Evaluate side-chains 131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 154 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 520 HIS A 929 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.199511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175420 restraints weight = 10751.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179710 restraints weight = 6431.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181458 restraints weight = 4104.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181886 restraints weight = 3113.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182783 restraints weight = 3043.117| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7471 Z= 0.130 Angle : 0.638 8.748 10187 Z= 0.312 Chirality : 0.042 0.336 1220 Planarity : 0.005 0.052 1278 Dihedral : 7.453 58.959 1193 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.41 % Allowed : 23.44 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.19 (0.27), residues: 958 helix: 0.41 (0.22), residues: 568 sheet: -1.03 (0.82), residues: 45 loop : -2.86 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.018 0.001 TYR A 797 PHE 0.025 0.002 PHE A 798 TRP 0.009 0.001 TRP A 863 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7466) covalent geometry : angle 0.62324 (10172) hydrogen bonds : bond 0.03733 ( 407) hydrogen bonds : angle 4.83080 ( 1191) link_BETA1-4 : bond 0.00600 ( 4) link_BETA1-4 : angle 2.51364 ( 12) link_NAG-ASN : bond 0.01459 ( 1) link_NAG-ASN : angle 6.27068 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3508 (tptt) cc_final: 0.3255 (mmtm) REVERT: A 602 ARG cc_start: 0.4564 (mmt180) cc_final: 0.2924 (ptp-170) REVERT: A 789 ASP cc_start: 0.6778 (m-30) cc_final: 0.6503 (m-30) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.0713 time to fit residues: 13.6016 Evaluate side-chains 128 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.189588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165337 restraints weight = 11183.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167545 restraints weight = 7656.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170182 restraints weight = 5352.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170534 restraints weight = 4047.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170676 restraints weight = 3686.467| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7471 Z= 0.263 Angle : 0.795 9.918 10187 Z= 0.390 Chirality : 0.048 0.407 1220 Planarity : 0.006 0.071 1278 Dihedral : 7.758 53.333 1193 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 5.82 % Allowed : 22.87 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.82 (0.26), residues: 958 helix: -0.18 (0.21), residues: 581 sheet: -0.69 (0.88), residues: 44 loop : -3.14 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 603 TYR 0.019 0.002 TYR A 452 PHE 0.036 0.003 PHE A 798 TRP 0.013 0.002 TRP A 129 HIS 0.013 0.002 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 7466) covalent geometry : angle 0.78076 (10172) hydrogen bonds : bond 0.04453 ( 407) hydrogen bonds : angle 5.06729 ( 1191) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 3.05923 ( 12) link_NAG-ASN : bond 0.01301 ( 1) link_NAG-ASN : angle 6.44916 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3566 (tptt) cc_final: 0.3275 (mmtm) REVERT: A 602 ARG cc_start: 0.4887 (mmt180) cc_final: 0.3136 (ptp-170) outliers start: 41 outliers final: 31 residues processed: 149 average time/residue: 0.0722 time to fit residues: 15.4276 Evaluate side-chains 141 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1145 PHE Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.195845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173027 restraints weight = 10722.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.176452 restraints weight = 6290.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.178202 restraints weight = 4197.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178848 restraints weight = 3398.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179611 restraints weight = 2943.245| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7471 Z= 0.130 Angle : 0.672 10.778 10187 Z= 0.325 Chirality : 0.043 0.352 1220 Planarity : 0.005 0.052 1278 Dihedral : 7.126 54.588 1193 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.12 % Allowed : 25.85 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.29 (0.27), residues: 958 helix: 0.31 (0.21), residues: 577 sheet: -0.89 (0.83), residues: 45 loop : -2.95 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.020 0.001 TYR A 452 PHE 0.021 0.001 PHE A 798 TRP 0.020 0.002 TRP A 948 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7466) covalent geometry : angle 0.65737 (10172) hydrogen bonds : bond 0.03677 ( 407) hydrogen bonds : angle 4.79937 ( 1191) link_BETA1-4 : bond 0.00559 ( 4) link_BETA1-4 : angle 2.93021 ( 12) link_NAG-ASN : bond 0.01368 ( 1) link_NAG-ASN : angle 6.00911 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8649 (mp10) cc_final: 0.8316 (mp10) REVERT: A 158 MET cc_start: 0.7979 (ttp) cc_final: 0.7588 (ttm) REVERT: A 602 ARG cc_start: 0.4741 (mmt180) cc_final: 0.3057 (ptp-170) REVERT: A 789 ASP cc_start: 0.6254 (m-30) cc_final: 0.5767 (m-30) REVERT: A 979 ASN cc_start: 0.7497 (t0) cc_final: 0.7244 (t0) REVERT: A 1086 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6977 (mp) outliers start: 29 outliers final: 22 residues processed: 133 average time/residue: 0.0669 time to fit residues: 13.1300 Evaluate side-chains 127 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.196667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.173802 restraints weight = 10631.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.177384 restraints weight = 6148.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178911 restraints weight = 4035.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179546 restraints weight = 3184.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.180905 restraints weight = 2928.141| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7471 Z= 0.130 Angle : 0.657 11.951 10187 Z= 0.319 Chirality : 0.042 0.344 1220 Planarity : 0.005 0.050 1278 Dihedral : 6.754 54.390 1193 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.12 % Allowed : 26.56 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.05 (0.27), residues: 958 helix: 0.52 (0.22), residues: 578 sheet: -0.94 (0.83), residues: 45 loop : -2.89 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.017 0.001 TYR A 452 PHE 0.020 0.001 PHE A 798 TRP 0.017 0.001 TRP A 948 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7466) covalent geometry : angle 0.64228 (10172) hydrogen bonds : bond 0.03511 ( 407) hydrogen bonds : angle 4.68683 ( 1191) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 2.84961 ( 12) link_NAG-ASN : bond 0.01280 ( 1) link_NAG-ASN : angle 5.97410 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8701 (mp10) cc_final: 0.8415 (mp10) REVERT: A 575 LEU cc_start: 0.7899 (mm) cc_final: 0.7551 (mm) REVERT: A 602 ARG cc_start: 0.4575 (mmt180) cc_final: 0.2661 (ptp-170) REVERT: A 789 ASP cc_start: 0.6353 (m-30) cc_final: 0.5916 (m-30) outliers start: 29 outliers final: 22 residues processed: 131 average time/residue: 0.0719 time to fit residues: 13.4770 Evaluate side-chains 124 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.197698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174849 restraints weight = 10674.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.178571 restraints weight = 6160.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.180244 restraints weight = 3942.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.180679 restraints weight = 3166.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.182196 restraints weight = 2876.917| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7471 Z= 0.123 Angle : 0.660 13.091 10187 Z= 0.319 Chirality : 0.042 0.369 1220 Planarity : 0.004 0.050 1278 Dihedral : 6.520 54.140 1193 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.12 % Allowed : 26.70 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.82 (0.27), residues: 958 helix: 0.75 (0.22), residues: 571 sheet: -1.19 (0.80), residues: 47 loop : -2.78 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.016 0.001 TYR A 452 PHE 0.020 0.001 PHE A 798 TRP 0.038 0.002 TRP A 948 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7466) covalent geometry : angle 0.64545 (10172) hydrogen bonds : bond 0.03434 ( 407) hydrogen bonds : angle 4.59364 ( 1191) link_BETA1-4 : bond 0.00484 ( 4) link_BETA1-4 : angle 2.80081 ( 12) link_NAG-ASN : bond 0.01297 ( 1) link_NAG-ASN : angle 5.85558 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.273 Fit side-chains REVERT: A 156 GLN cc_start: 0.8613 (mp10) cc_final: 0.8369 (mp10) REVERT: A 158 MET cc_start: 0.7820 (ttp) cc_final: 0.7448 (ttm) REVERT: A 373 TYR cc_start: 0.6876 (t80) cc_final: 0.6028 (t80) REVERT: A 575 LEU cc_start: 0.7856 (mm) cc_final: 0.7641 (mm) REVERT: A 598 MET cc_start: 0.7731 (mmp) cc_final: 0.7457 (mmp) REVERT: A 602 ARG cc_start: 0.4448 (mmt180) cc_final: 0.2752 (ptp-170) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.0717 time to fit residues: 12.6942 Evaluate side-chains 121 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.197851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174334 restraints weight = 10847.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177409 restraints weight = 6700.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178709 restraints weight = 4703.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179579 restraints weight = 3613.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.180490 restraints weight = 3250.791| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7471 Z= 0.135 Angle : 0.664 13.638 10187 Z= 0.320 Chirality : 0.043 0.424 1220 Planarity : 0.004 0.050 1278 Dihedral : 6.381 53.782 1193 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.98 % Allowed : 26.70 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.80 (0.27), residues: 958 helix: 0.75 (0.22), residues: 576 sheet: -1.11 (0.80), residues: 47 loop : -2.78 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.021 0.001 TYR A 452 PHE 0.019 0.001 PHE A 798 TRP 0.022 0.002 TRP A 948 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7466) covalent geometry : angle 0.64999 (10172) hydrogen bonds : bond 0.03447 ( 407) hydrogen bonds : angle 4.61103 ( 1191) link_BETA1-4 : bond 0.00458 ( 4) link_BETA1-4 : angle 2.76324 ( 12) link_NAG-ASN : bond 0.01263 ( 1) link_NAG-ASN : angle 5.85487 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8537 (mp10) cc_final: 0.8317 (mp10) REVERT: A 373 TYR cc_start: 0.6862 (t80) cc_final: 0.6173 (t80) REVERT: A 575 LEU cc_start: 0.7981 (mm) cc_final: 0.7734 (mm) REVERT: A 598 MET cc_start: 0.7743 (mmp) cc_final: 0.7468 (mmp) REVERT: A 602 ARG cc_start: 0.4517 (mmt180) cc_final: 0.2667 (ptp-170) REVERT: A 1086 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7061 (mt) outliers start: 28 outliers final: 24 residues processed: 126 average time/residue: 0.0705 time to fit residues: 12.8094 Evaluate side-chains 122 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 0.0050 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 0.0370 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178278 restraints weight = 10569.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180703 restraints weight = 6165.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182766 restraints weight = 4375.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183462 restraints weight = 3383.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.184635 restraints weight = 2988.376| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7471 Z= 0.120 Angle : 0.656 14.264 10187 Z= 0.317 Chirality : 0.042 0.427 1220 Planarity : 0.004 0.050 1278 Dihedral : 6.209 53.696 1193 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.12 % Allowed : 26.99 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.63 (0.28), residues: 958 helix: 0.88 (0.22), residues: 576 sheet: -1.15 (0.79), residues: 45 loop : -2.69 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.022 0.001 TYR A 452 PHE 0.019 0.001 PHE A 798 TRP 0.022 0.001 TRP A 948 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7466) covalent geometry : angle 0.64199 (10172) hydrogen bonds : bond 0.03362 ( 407) hydrogen bonds : angle 4.54948 ( 1191) link_BETA1-4 : bond 0.00458 ( 4) link_BETA1-4 : angle 2.71175 ( 12) link_NAG-ASN : bond 0.01275 ( 1) link_NAG-ASN : angle 5.76214 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.265 Fit side-chains REVERT: A 158 MET cc_start: 0.7782 (ttp) cc_final: 0.7450 (ttm) REVERT: A 575 LEU cc_start: 0.7795 (mm) cc_final: 0.7582 (mm) REVERT: A 598 MET cc_start: 0.7678 (mmp) cc_final: 0.7468 (mmp) REVERT: A 602 ARG cc_start: 0.4284 (mmt180) cc_final: 0.2456 (ptp-170) REVERT: A 1086 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7033 (mt) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.0689 time to fit residues: 12.5779 Evaluate side-chains 122 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.200619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.177936 restraints weight = 10584.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.181593 restraints weight = 6203.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.184066 restraints weight = 3991.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.184388 restraints weight = 2896.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.185100 restraints weight = 2736.117| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7471 Z= 0.121 Angle : 0.665 14.477 10187 Z= 0.324 Chirality : 0.043 0.431 1220 Planarity : 0.004 0.047 1278 Dihedral : 6.041 53.526 1193 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.55 % Allowed : 27.27 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.51 (0.28), residues: 958 helix: 1.04 (0.22), residues: 567 sheet: -1.02 (0.79), residues: 45 loop : -2.68 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.021 0.001 TYR A 452 PHE 0.018 0.001 PHE A 798 TRP 0.017 0.001 TRP A 948 HIS 0.009 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7466) covalent geometry : angle 0.65221 (10172) hydrogen bonds : bond 0.03345 ( 407) hydrogen bonds : angle 4.52837 ( 1191) link_BETA1-4 : bond 0.00460 ( 4) link_BETA1-4 : angle 2.64727 ( 12) link_NAG-ASN : bond 0.01234 ( 1) link_NAG-ASN : angle 5.67705 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.67 seconds wall clock time: 22 minutes 27.07 seconds (1347.07 seconds total)